which one is PennCNV v2010May01 ? #64
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PennCNV is not in github around 2010 (This is not v1.0.0). I do not have a
copy of the 2010 version at hand; however, I believe that very minimal
changes are made to PennCNV CNV calling procedure itself (most changes are
for accessary programs, and for processing outputs or for increasing
compatibility with non-human species). I think you can just use the latest
version to do CNV calling.
…On Fri, Jan 1, 2021 at 11:18 AM Qidi Feng ***@***.***> wrote:
Hi Kai,
I am trying to use the same PennCNV version with a previously published
paper in order to make the cnv results more comparable? The PennCNV used in
that paper is PennCNV v2010May01. I am not sure which version is this? Is
this PennCNV v1.0.0?
Happy new year!
Best regards,
Qidi Feng
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Hi Kai,
Thank you very much for your reply! But now I got problems repeating
previous paper's calling results with almost the same pipeline. Would you
pls give me any hints?
The previous paper claims that they use "“hhall.hmm”, compile pfb from the
data, use gcmodel adjustment, using an older version of PennCNV
v2010May01". I connected with the author and got their inputs of 100
samples (containing BAF and LRR), I run PennCNVv1.0.5 with command "perl
detect_cnv.pl -test -hmm ../PennCNV-1.0.5/lib/hhall.hmm -pfb taiwan100.pfb
-gcmodel taiwan100.gc2 -listfile samplelist.txt -log rawcnv.log -out
taiwan100.rawcnv". I compared their raw cnv results with mine, and found
there are big differences in number of CNVs for some specific samples (for
example 9464294022_R03C01). You may like to check detailed results between
the two versions of results in the attached file.
The only difference in pipeline I can think of is 1. pfb file (I compiled
pfb file from the 100 samples while the previous paper should compile pfb
file from the original ~5000 samples) and 2. PennCNV version. Do you have
any suggestions explaining the differences on cnv results? Do you think PFB
file could potentially cause this difference?
Thanks again for your help! Happy new year!
Best,
Qidi
On Sat, Jan 2, 2021 at 12:13 AM Kai Wang ***@***.***> wrote:
PennCNV is not in github around 2010 (This is not v1.0.0). I do not have a
copy of the 2010 version at hand; however, I believe that very minimal
changes are made to PennCNV CNV calling procedure itself (most changes are
for accessary programs, and for processing outputs or for increasing
compatibility with non-human species). I think you can just use the latest
version to do CNV calling.
On Fri, Jan 1, 2021 at 11:18 AM Qidi Feng ***@***.***>
wrote:
> Hi Kai,
>
> I am trying to use the same PennCNV version with a previously published
> paper in order to make the cnv results more comparable? The PennCNV used
in
> that paper is PennCNV v2010May01. I am not sure which version is this? Is
> this PennCNV v1.0.0?
>
> Happy new year!
>
> Best regards,
> Qidi Feng
>
> —
> You are receiving this because you are subscribed to this thread.
> Reply to this email directly, view it on GitHub
> <#64>, or unsubscribe
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https://github.com/notifications/unsubscribe-auth/ABNG3OETC4OKB7KGZQWUSBLSXXYTZANCNFSM4VQLXVFQ
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>
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.
chr6:57587550-57620876 numsnp=3 length=33,327 state1,cn=0 3999879003_R02C01 startsnp=psy_rs146333445 endsnp=psy_rs145112474 conf=6.560
chr7:70419818-70422360 numsnp=3 length=2,543 state1,cn=0 3999879003_R02C01 startsnp=rs1464853 endsnp=psy_rs60233550 conf=9.012
chr16:3613019-3613263 numsnp=5 length=245 state1,cn=0 3999879003_R02C01 startsnp=exm1211533 endsnp=exm1211547 conf=14.304
chr16:70045749-70089450 numsnp=3 length=43,702 state1,cn=0 3999879003_R02C01 startsnp=psy_rs11648231 endsnp=psy_rs150266884 conf=6.804
chr5:70307162-70308607 numsnp=9 length=1,446 state2,cn=1 3999879003_R02C01 startsnp=exm459256 endsnp=variant.85123 conf=8.043
chr15:84700097-84706544 numsnp=14 length=6,448 state2,cn=1 3999879003_R02C01 startsnp=exm1184260 endsnp=exm1184280 conf=29.454
chr21:37107446-37195391 numsnp=8 length=87,946 state2,cn=1 3999879003_R02C01 startsnp=rs2835109 endsnp=rs2222963 conf=17.425
chr1:12919081-13187294 numsnp=29 length=268,214 state5,cn=3 3999879003_R02C01 startsnp=exm17491 endsnp=kgp3971131 conf=31.216
chr1:97735667-97757424 numsnp=5 length=21,758 state5,cn=3 3999879003_R02C01 startsnp=rs1520668 endsnp=rs10465748 conf=3.974
chr1:117983815-117989275 numsnp=3 length=5,461 state5,cn=3 3999879003_R02C01 startsnp=rs10923297 endsnp=rs4659050 conf=4.682
chr2:20096767-20113967 numsnp=15 length=17,201 state5,cn=3 3999879003_R02C01 startsnp=exm174761 endsnp=exm174823 conf=6.807
chr2:39278400-39305489 numsnp=11 length=27,090 state5,cn=3 3999879003_R02C01 startsnp=exm188386 endsnp=rs297136 conf=12.072
chr2:55539905-55573401 numsnp=18 length=33,497 state5,cn=3 3999879003_R02C01 startsnp=rs10189439 endsnp=exm195158 conf=15.472
chr2:61472345-61508231 numsnp=14 length=35,887 state5,cn=3 3999879003_R02C01 startsnp=exm196534 endsnp=exm2255436 conf=7.958
chr2:62193438-62235524 numsnp=5 length=42,087 state5,cn=3 3999879003_R02C01 startsnp=rs11677744 endsnp=psy_rs5019426 conf=6.815
chr2:145463764-145540283 numsnp=6 length=76,520 state5,cn=3 3999879003_R02C01 startsnp=rs2195114 endsnp=psy_rs144473890 conf=4.952
chr2:154058372-154173881 numsnp=14 length=115,510 state5,cn=3 3999879003_R02C01 startsnp=rs4664649 endsnp=rs13021542 conf=13.340
chr3:155539266-155560337 numsnp=8 length=21,072 state5,cn=3 3999879003_R02C01 startsnp=rs11921267 endsnp=exm2042129 conf=0.000
chr3:160119716-160143943 numsnp=26 length=24,228 state5,cn=3 3999879003_R02C01 startsnp=newrs141089654 endsnp=exm361926 conf=13.113
chr3:188112554-188116784 numsnp=3 length=4,231 state5,cn=3 3999879003_R02C01 startsnp=exm-rs1464510 endsnp=rs9820681 conf=0.000
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chr4:104053867-104062206 numsnp=15 length=8,340 state5,cn=3 3999879003_R02C01 startsnp=exm416552 endsnp=exm416602 conf=13.232
chr4:161875145-161927775 numsnp=4 length=52,631 state5,cn=3 3999879003_R02C01 startsnp=rs4529002 endsnp=psy_rs80120634 conf=0.872
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chr4:167571068-167663664 numsnp=13 length=92,597 state5,cn=3 3999879003_R02C01 startsnp=rs28713613 endsnp=rs7691894 conf=12.811
chr5:77458150-77523963 numsnp=11 length=65,814 state5,cn=3 3999879003_R02C01 startsnp=rs4704484 endsnp=variant.85363 conf=13.039
chr5:103771206-103838556 numsnp=6 length=67,351 state5,cn=3 3999879003_R02C01 startsnp=rs1442111 endsnp=rs11747766 conf=8.957
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chrX:126157448-126249850 numsnp=9 length=92,403 state5,cn=3 3999879003_R02C01 startsnp=rs5930059 endsnp=rs11096073 conf=2.921
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chr3:160119716-160143943 numsnp=26 length=24,228 state5,cn=3 3999879003_R09C02 startsnp=newrs141089654 endsnp=exm361926 conf=15.249
chr3:163096848-163233510 numsnp=7 length=136,663 state5,cn=3 3999879003_R09C02 startsnp=rs6796340 endsnp=rs6765213 conf=10.536
chr3:171722897-171738987 numsnp=3 length=16,091 state5,cn=3 3999879003_R09C02 startsnp=psy_rs186068546 endsnp=rs472728 conf=0.000
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chr4:165403992-165422101 numsnp=3 length=18,110 state5,cn=3 3999879003_R09C02 startsnp=rs7690372 endsnp=rs1505392 conf=6.295
chr5:20740586-20865083 numsnp=7 length=124,498 state5,cn=3 3999879003_R09C02 startsnp=rs10941853 endsnp=rs7442892 conf=11.909
chr5:77458150-77579205 numsnp=14 length=121,056 state5,cn=3 3999879003_R09C02 startsnp=rs4704484 endsnp=rs10062813 conf=15.452
chr5:139931633-139931740 numsnp=20 length=108 state5,cn=3 3999879003_R09C02 startsnp=exm2088587 endsnp=exm482463 conf=22.537
chr6:7373356-7374207 numsnp=9 length=852 state5,cn=3 3999879003_R09C02 startsnp=exm514682 endsnp=exm514705 conf=8.446
chr6:54278274-54297588 numsnp=4 length=19,315 state5,cn=3 3999879003_R09C02 startsnp=rs3907818 endsnp=rs515020 conf=4.553
chr7:80699883-80718358 numsnp=5 length=18,476 state5,cn=3 3999879003_R09C02 startsnp=rs6944056 endsnp=rs2697949 conf=0.316
chr7:87249057-87418861 numsnp=11 length=169,805 state5,cn=3 3999879003_R09C02 startsnp=psy_rs60191129 endsnp=rs1029421 conf=11.064
chr9:30187798-30219494 numsnp=4 length=31,697 state5,cn=3 3999879003_R09C02 startsnp=rs7868434 endsnp=rs2769643 conf=0.000
chr9:109581132-109626324 numsnp=4 length=45,193 state5,cn=3 3999879003_R09C02 startsnp=rs4742675 endsnp=psy_rs140614785 conf=2.744
chr10:7899231-7923508 numsnp=3 length=24,278 state5,cn=3 3999879003_R09C02 startsnp=rs10905239 endsnp=rs1244461 conf=4.238
chr10:18854946-18859719 numsnp=5 length=4,774 state5,cn=3 3999879003_R09C02 startsnp=psy_rs149783287 endsnp=psy_rs140397060 conf=0.000
chr10:27311557-27322303 numsnp=5 length=10,747 state5,cn=3 3999879003_R09C02 startsnp=exm815981 endsnp=exm815999 conf=9.868
chr10:56790969-56817533 numsnp=3 length=26,565 state5,cn=3 3999879003_R09C02 startsnp=exm-rs10740609 endsnp=rs17528196 conf=3.661
chr10:112753721-112773079 numsnp=5 length=19,359 state5,cn=3 3999879003_R09C02 startsnp=rs6585026 endsnp=rs1327552 conf=0.970
chr11:39981948-40015352 numsnp=4 length=33,405 state5,cn=3 3999879003_R09C02 startsnp=rs10837311 endsnp=exm2267171 conf=6.013
chr12:77943018-77949236 numsnp=3 length=6,219 state5,cn=3 3999879003_R09C02 startsnp=rs10437872 endsnp=rs7308700 conf=6.393
chr13:114930955-114939396 numsnp=4 length=8,442 state5,cn=3 3999879003_R09C02 startsnp=rs423237 endsnp=rs11147317 conf=2.993
chr15:24606732-24668007 numsnp=4 length=61,276 state5,cn=3 3999879003_R09C02 startsnp=rs12915627 endsnp=rs7174746 conf=10.592
chr16:28616665-28621318 numsnp=10 length=4,654 state5,cn=3 3999879003_R09C02 startsnp=rs4788069 endsnp=kgp16473159 conf=15.849
chr17:34436708-34477887 numsnp=14 length=41,180 state5,cn=3 3999879003_R09C02 startsnp=rs957979 endsnp=rs4796168 conf=20.089
chr19:53334239-53345371 numsnp=17 length=11,133 state5,cn=3 3999879003_R09C02 startsnp=psy_rs10411500 endsnp=exm1500433 conf=15.152
chr19:54844047-54845031 numsnp=6 length=985 state5,cn=3 3999879003_R09C02 startsnp=rs885733 endsnp=exm1504424 conf=7.462
chr22:26132612-26146429 numsnp=4 length=13,818 state5,cn=3 3999879003_R09C02 startsnp=rs10212011 endsnp=rs11090409 conf=8.007
chrX:35873056-36007614 numsnp=27 length=134,559 state5,cn=3 3999879003_R09C02 startsnp=rs2336401 endsnp=rs6629027 conf=13.044
chrX:79325880-79389391 numsnp=10 length=63,512 state5,cn=3 3999879003_R09C02 startsnp=rs74948985 endsnp=rs589133 conf=3.529
chrX:83116204-83130202 numsnp=16 length=13,999 state5,cn=3 3999879003_R09C02 startsnp=exm1647875 endsnp=rs5922001 conf=4.933
chrX:84122736-84195135 numsnp=6 length=72,400 state5,cn=3 3999879003_R09C02 startsnp=rs6623190 endsnp=rs613906 conf=1.750
chrX:84685904-84706371 numsnp=4 length=20,468 state5,cn=3 3999879003_R09C02 startsnp=rs6623289 endsnp=rs6623302 conf=0.446
chrX:121412951-121591571 numsnp=21 length=178,621 state5,cn=3 3999879003_R09C02 startsnp=rs2495668 endsnp=rs4825454 conf=15.264
chrX:126211747-126287592 numsnp=9 length=75,846 state5,cn=3 3999879003_R09C02 startsnp=rs5931832 endsnp=rs203499 conf=4.236
chr6:57587550-57620876 numsnp=3 length=33,327 state1,cn=0 3999879015_R02C02 startsnp=psy_rs146333445 endsnp=psy_rs145112474 conf=6.686
chr22:50228087-50239154 numsnp=6 length=11,068 state1,cn=0 3999879015_R02C02 startsnp=psy_rs138892 endsnp=psy_rs11704466 conf=19.856
chr3:1929666-1949594 numsnp=6 length=19,929 state2,cn=1 3999879015_R02C02 startsnp=rs11713534 endsnp=rs9821217 conf=12.179
chr3:52474473-52477866 numsnp=11 length=3,394 state2,cn=1 3999879015_R02C02 startsnp=exm321379 endsnp=exm2261511 conf=25.322
chr5:139931607-139931661 numsnp=25 length=55 state2,cn=1 3999879015_R02C02 startsnp=exm482409 endsnp=exm482455 conf=39.074
chr10:58916759-58938552 numsnp=5 length=21,794 state2,cn=1 3999879015_R02C02 startsnp=rs6481254 endsnp=rs6481257 conf=9.349
chr11:10313693-10327884 numsnp=3 length=14,192 state2,cn=1 3999879015_R02C02 startsnp=psy_rs7123078 endsnp=exm890283 conf=8.693
chr15:85437286-85448906 numsnp=22 length=11,621 state2,cn=1 3999879015_R02C02 startsnp=rs8037320 endsnp=rs2290269 conf=31.331
chr16:605481-606913 numsnp=3 length=1,433 state2,cn=1 3999879015_R02C02 startsnp=exm2272332 endsnp=psy_rs4984889 conf=6.680
chr21:15214708-15395187 numsnp=16 length=180,480 state2,cn=1 3999879015_R02C02 startsnp=rs3115511 endsnp=rs2822379 conf=32.067
chr3:191408742-191423639 numsnp=3 length=14,898 state5,cn=3 3999879015_R02C02 startsnp=rs6772065 endsnp=rs1083696 conf=10.578
chr4:144944926-145038131 numsnp=10 length=93,206 state5,cn=3 3999879015_R02C02 startsnp=psy_rs143716890 endsnp=variant.82937 conf=20.249
chr6:145027648-145051599 numsnp=6 length=23,952 state5,cn=3 3999879015_R02C02 startsnp=rs6927255 endsnp=exm584040 conf=13.569
chr8:7308356-7347711 numsnp=6 length=39,356 state5,cn=3 3999879015_R02C02 startsnp=indel.99556 endsnp=kgp28743309 conf=10.053
chr8:110765282-110821596 numsnp=8 length=56,315 state5,cn=3 3999879015_R02C02 startsnp=rs2350101 endsnp=rs12548341 conf=13.815
chr9:39098698-39103792 numsnp=4 length=5,095 state5,cn=3 3999879015_R02C02 startsnp=rs4961901 endsnp=var_9_39103791 conf=11.997
chr11:89986667-90050248 numsnp=7 length=63,582 state5,cn=3 3999879015_R02C02 startsnp=rs7101892 endsnp=rs495395 conf=12.934
chr11:97431300-97443131 numsnp=3 length=11,832 state5,cn=3 3999879015_R02C02 startsnp=rs11227014 endsnp=rs2852921 conf=1.407
chr12:133046268-133046915 numsnp=4 length=648 state5,cn=3 3999879015_R02C02 startsnp=psy_rs12228614 endsnp=psy_rs4883588 conf=0.000
chr16:28616665-28754684 numsnp=17 length=138,020 state5,cn=3 3999879015_R02C02 startsnp=rs4788069 endsnp=kgp2091645 conf=14.571
chr19:8334280-8339547 numsnp=3 length=5,268 state5,cn=3 3999879015_R02C02 startsnp=rs250508 endsnp=psy_rs76624499 conf=4.797
chrX:146119530-146328831 numsnp=16 length=209,302 state5,cn=3 3999879015_R02C02 startsnp=rs12010143 endsnp=rs5951956 conf=6.633
chrX:151598719-151600057 numsnp=3 length=1,339 state5,cn=3 3999879015_R02C02 startsnp=rs5969896 endsnp=rs12688305 conf=0.269
chr2:194691051-194694686 numsnp=3 length=3,636 state1,cn=0 3999879015_R03C02 startsnp=psy_rs73984715 endsnp=psy_rs12987240 conf=13.303
chr5:139931607-139931618 numsnp=4 length=12 state1,cn=0 3999879015_R03C02 startsnp=exm482409 endsnp=exm482420 conf=16.016
chr16:70045749-70089450 numsnp=3 length=43,702 state1,cn=0 3999879015_R03C02 startsnp=psy_rs11648231 endsnp=psy_rs150266884 conf=8.044
chr22:50228087-50239154 numsnp=6 length=11,068 state1,cn=0 3999879015_R03C02 startsnp=psy_rs138892 endsnp=psy_rs11704466 conf=21.375
chr1:189350700-189542729 numsnp=11 length=192,030 state2,cn=1 3999879015_R03C02 startsnp=rs16830499 endsnp=rs269747 conf=43.213
chr1:196738732-196887530 numsnp=32 length=148,799 state2,cn=1 3999879015_R03C02 startsnp=psy_rs12039050 endsnp=variant.9073 conf=63.461
chr2:40948151-40949168 numsnp=3 length=1,018 state2,cn=1 3999879015_R03C02 startsnp=rs10211572 endsnp=rs1107932 conf=6.294
chr5:139931619-139931661 numsnp=21 length=43 state2,cn=1 3999879015_R03C02 startsnp=exm482421 endsnp=exm482455 conf=40.485
chr6:57262543-57318492 numsnp=4 length=55,950 state2,cn=1 3999879015_R03C02 startsnp=kgp3823064 endsnp=psy_rs186922526 conf=8.409
chr6:159145196-159171342 numsnp=8 length=26,147 state2,cn=1 3999879015_R03C02 startsnp=rs7751477 endsnp=rs3123093 conf=13.271
chr16:16633361-16641261 numsnp=3 length=7,901 state2,cn=1 3999879015_R03C02 startsnp=rs16955286 endsnp=psy_rs28395512 conf=5.060
chr3:19401472-19407684 numsnp=3 length=6,213 state5,cn=3 3999879015_R03C02 startsnp=rs17005867 endsnp=rs6783450 conf=0.000
chr5:744005-825329 numsnp=16 length=81,325 state5,cn=3 3999879015_R03C02 startsnp=kgp4423575 endsnp=exm441004 conf=13.029
chr7:44935-67365 numsnp=7 length=22,431 state5,cn=3 3999879015_R03C02 startsnp=rs7456436 endsnp=rs3924854 conf=17.908
chr8:78093837-78103417 numsnp=4 length=9,581 state5,cn=3 3999879015_R03C02 startsnp=exm-rs7821178 endsnp=rs2167730 conf=12.355
chr11:5905557-5908939 numsnp=18 length=3,383 state5,cn=3 3999879015_R03C02 startsnp=exm884118 endsnp=rs1453433 conf=28.612
chr12:133046268-133046348 numsnp=3 length=81 state5,cn=3 3999879015_R03C02 startsnp=psy_rs12228614 endsnp=psy_rs117276632 conf=9.338
chr14:106067618-106127330 numsnp=5 length=59,713 state5,cn=3 3999879015_R03C02 startsnp=rs12884681 endsnp=kgp4991126 conf=11.442
chr15:22368588-22468503 numsnp=27 length=99,916 state5,cn=3 3999879015_R03C02 startsnp=exm1140790 endsnp=rs4462663 conf=13.468
chr16:28616665-28621318 numsnp=10 length=4,654 state5,cn=3 3999879015_R03C02 startsnp=rs4788069 endsnp=kgp16473159 conf=17.616
chr17:15884428-15929933 numsnp=15 length=45,506 state5,cn=3 3999879015_R03C02 startsnp=indel.44804 endsnp=exm1297463 conf=25.316
chr18:75817704-75829588 numsnp=4 length=11,885 state5,cn=3 3999879015_R03C02 startsnp=rs7228984 endsnp=rs4422056 conf=13.189
chrX:2343284-2408593 numsnp=18 length=65,310 state2,cn=1 3999879015_R03C02 startsnp=variant.107618 endsnp=kgp31005848 conf=9.677
chrX:27030478-27038898 numsnp=3 length=8,421 state5,cn=3 3999879015_R03C02 startsnp=rs6628227 endsnp=rs974891 conf=2.072
chrX:75954458-76096727 numsnp=8 length=142,270 state5,cn=3 3999879015_R03C02 startsnp=rs12854715 endsnp=rs233013 conf=8.326
chrX:84140833-84152731 numsnp=3 length=11,899 state5,cn=3 3999879015_R03C02 startsnp=rs1517192 endsnp=rs1010796 conf=1.800
chrX:125871040-125893561 numsnp=4 length=22,522 state5,cn=3 3999879015_R03C02 startsnp=rs1112075 endsnp=rs12834033 conf=3.929
chrX:146119530-146328831 numsnp=16 length=209,302 state5,cn=3 3999879015_R03C02 startsnp=rs12010143 endsnp=rs5951956 conf=10.320
chr1:243803714-243813097 numsnp=3 length=9,384 state1,cn=0 3999879053_R11C01 startsnp=psy_rs1486472 endsnp=psy_rs77030218 conf=6.902
chr4:102928866-102931282 numsnp=3 length=2,417 state1,cn=0 3999879053_R11C01 startsnp=psy_rs13113094 endsnp=psy_rs143152246 conf=4.409
chr5:49466231-49470705 numsnp=6 length=4,475 state1,cn=0 3999879053_R11C01 startsnp=psy_rs147936069 endsnp=psy_rs11953045 conf=14.063
chr5:139072030-139086651 numsnp=3 length=14,622 state1,cn=0 3999879053_R11C01 startsnp=psy_rs114462231 endsnp=psy_rs2133561 conf=11.727
chr22:50228087-50239154 numsnp=6 length=11,068 state1,cn=0 3999879053_R11C01 startsnp=psy_rs138892 endsnp=psy_rs11704466 conf=18.732
chr5:70307162-70308607 numsnp=9 length=1,446 state2,cn=1 3999879053_R11C01 startsnp=exm459256 endsnp=variant.85123 conf=7.946
chr5:115525539-115533407 numsnp=3 length=7,869 state2,cn=1 3999879053_R11C01 startsnp=rs7733187 endsnp=rs10037375 conf=6.325
chr9:11909707-12013711 numsnp=14 length=104,005 state2,cn=1 3999879053_R11C01 startsnp=psy_rs190506132 endsnp=rs10756313 conf=49.237
chr11:67533195-67731956 numsnp=11 length=198,762 state2,cn=1 3999879053_R11C01 startsnp=rs10750808 endsnp=rs308351 conf=17.664
chr15:20177092-20192086 numsnp=6 length=14,995 state2,cn=1 3999879053_R11C01 startsnp=rs12440100 endsnp=rs4932078 conf=14.490
chr15:34727994-34800595 numsnp=5 length=72,602 state2,cn=1 3999879053_R11C01 startsnp=psy_rs79184910 endsnp=rs4924714 conf=10.314
chr19:43344686-43529105 numsnp=50 length=184,420 state2,cn=1 3999879053_R11C01 startsnp=exm2272793 endsnp=indel.56144 conf=27.624
chr1:752566-838555 numsnp=5 length=85,990 state5,cn=3 3999879053_R11C01 startsnp=rs3094315 endsnp=rs4970383 conf=10.070
chr3:75597273-75727056 numsnp=3 length=129,784 state5,cn=3 3999879053_R11C01 startsnp=psy_rs62258771 endsnp=rs352398 conf=2.981
chr3:181383366-181400102 numsnp=3 length=16,737 state5,cn=3 3999879053_R11C01 startsnp=rs11927844 endsnp=psy_rs11923447 conf=6.538
chr8:114885413-114892901 numsnp=3 length=7,489 state5,cn=3 3999879053_R11C01 startsnp=rs13258552 endsnp=rs7833314 conf=6.229
chr16:16633361-16832414 numsnp=4 length=199,054 state5,cn=3 3999879053_R11C01 startsnp=rs16955286 endsnp=rs10500401 conf=6.091
chr16:18601266-18608061 numsnp=3 length=6,796 state5,cn=3 3999879053_R11C01 startsnp=rs9939825 endsnp=kgp560859 conf=6.168
chr17:6866978-6889557 numsnp=5 length=22,580 state5,cn=3 3999879053_R11C01 startsnp=rs1605441 endsnp=rs6502998 conf=5.688
chr17:20364207-20387785 numsnp=5 length=23,579 state5,cn=3 3999879053_R11C01 startsnp=kgp500265 endsnp=psy_rs75150763 conf=10.982
chr18:64941776-64967509 numsnp=5 length=25,734 state5,cn=3 3999879053_R11C01 startsnp=rs12457479 endsnp=rs9319727 conf=11.967
chrX:89662079-89824761 numsnp=7 length=162,683 state1,cn=0 3999879053_R11C01 startsnp=kgp22803046 endsnp=rs2755514 conf=5.886
chrX:88624635-88711468 numsnp=5 length=86,834 state3,cn=2 3999879053_R11C01 startsnp=rs5942523 endsnp=rs5942583 conf=12.399
chrX:91015570-91068591 numsnp=4 length=53,022 state3,cn=2 3999879053_R11C01 startsnp=kgp22755926 endsnp=kgp22793616 conf=9.515
chr2:194691051-194694686 numsnp=3 length=3,636 state1,cn=0 3999899096_R06C01 startsnp=psy_rs73984715 endsnp=psy_rs12987240 conf=9.538
chr4:173424803-173429510 numsnp=4 length=4,708 state1,cn=0 3999899096_R06C01 startsnp=rs2124204 endsnp=psy_rs112429191 conf=8.769
chr8:39284717-39390219 numsnp=6 length=105,503 state1,cn=0 3999899096_R06C01 startsnp=psy_rs7827037 endsnp=rs7829181 conf=25.289
chr22:50228087-50237366 numsnp=4 length=9,280 state1,cn=0 3999899096_R06C01 startsnp=psy_rs138892 endsnp=psy_rs5769748 conf=19.228
chr9:11909707-12013711 numsnp=14 length=104,005 state2,cn=1 3999899096_R06C01 startsnp=psy_rs190506132 endsnp=rs10756313 conf=32.784
chr11:81509575-81516733 numsnp=4 length=7,159 state2,cn=1 3999899096_R06C01 startsnp=rs1542465 endsnp=rs11232877 conf=12.142
chr13:89817399-89833815 numsnp=4 length=16,417 state2,cn=1 3999899096_R06C01 startsnp=rs9522451 endsnp=psy_rs1854759 conf=2.072
chr1:97742655-97757424 numsnp=4 length=14,770 state5,cn=3 3999899096_R06C01 startsnp=psy_rs142444049 endsnp=rs10465748 conf=6.769
chr1:194492493-194530914 numsnp=5 length=38,422 state5,cn=3 3999899096_R06C01 startsnp=rs2494316 endsnp=rs3001167 conf=11.561
chr3:90402558-90499969 numsnp=5 length=97,412 state5,cn=3 3999899096_R06C01 startsnp=rs9856545 endsnp=kgp17585513 conf=7.378
chr4:163032521-163044149 numsnp=4 length=11,629 state5,cn=3 3999899096_R06C01 startsnp=exm432144 endsnp=rs17041987 conf=2.983
chr5:730271-816849 numsnp=8 length=86,579 state5,cn=3 3999899096_R06C01 startsnp=rs436354 endsnp=rs3890125 conf=16.361
chr7:44935-67365 numsnp=7 length=22,431 state5,cn=3 3999899096_R06C01 startsnp=rs7456436 endsnp=rs3924854 conf=11.133
chr12:6031943-6058257 numsnp=7 length=26,315 state5,cn=3 3999899096_R06C01 startsnp=exm976450 endsnp=exm1781530 conf=9.841
chr12:75900382-75925776 numsnp=8 length=25,395 state5,cn=3 3999899096_R06C01 startsnp=exm1022737 endsnp=rs10879928 conf=10.029
chrX:89662079-89824761 numsnp=7 length=162,683 state1,cn=0 3999899096_R06C01 startsnp=kgp22803046 endsnp=rs2755514 conf=5.454
chrX:47911871-47920248 numsnp=17 length=8,378 state3,cn=2 3999899096_R06C01 startsnp=rs5906535 endsnp=exm1637165 conf=13.093
chr2:194691051-194694686 numsnp=3 length=3,636 state1,cn=0 3999899096_R09C02 startsnp=psy_rs73984715 endsnp=psy_rs12987240 conf=8.643
chr5:139072030-139086651 numsnp=3 length=14,622 state1,cn=0 3999899096_R09C02 startsnp=psy_rs114462231 endsnp=psy_rs2133561 conf=10.903
chr20:37009923-37029825 numsnp=3 length=19,903 state1,cn=0 3999899096_R09C02 startsnp=rs737091 endsnp=rs1780634 conf=8.633
chr22:50228087-50239154 numsnp=6 length=11,068 state1,cn=0 3999899096_R09C02 startsnp=psy_rs138892 endsnp=psy_rs11704466 conf=21.814
chr3:164101193-164109377 numsnp=4 length=8,185 state2,cn=1 3999899096_R09C02 startsnp=rs721976 endsnp=rs7616947 conf=14.352
chr6:78967569-79024097 numsnp=7 length=56,529 state2,cn=1 3999899096_R09C02 startsnp=psy_rs818244 endsnp=psy_rs62425481 conf=18.518
chr8:130123196-130130604 numsnp=4 length=7,409 state2,cn=1 3999899096_R09C02 startsnp=rs6987260 endsnp=rs6470697 conf=14.456
chr9:88833465-88842933 numsnp=11 length=9,469 state2,cn=1 3999899096_R09C02 startsnp=rs4316216 endsnp=exm758916 conf=28.184
chr13:57711035-57822208 numsnp=6 length=111,174 state2,cn=1 3999899096_R09C02 startsnp=rs602296 endsnp=rs1331752 conf=18.338
chr1:110230278-110233147 numsnp=5 length=2,870 state5,cn=3 3999899096_R09C02 startsnp=psy_rs36208869 endsnp=exm-rs1056806 conf=3.188
chr1:194451226-194492493 numsnp=3 length=41,268 state5,cn=3 3999899096_R09C02 startsnp=psy_rs66655024 endsnp=rs2494316 conf=8.155
chr3:19384135-19407684 numsnp=5 length=23,550 state5,cn=3 3999899096_R09C02 startsnp=exm294836 endsnp=rs6783450 conf=1.578
chr5:17225333-17249420 numsnp=3 length=24,088 state5,cn=3 3999899096_R09C02 startsnp=rs2242415 endsnp=rs953431 conf=8.678
chr7:87259385-87418861 numsnp=10 length=159,477 state5,cn=3 3999899096_R09C02 startsnp=psy_rs6963426 endsnp=rs1029421 conf=13.538
chr10:18331664-18338686 numsnp=4 length=7,023 state5,cn=3 3999899096_R09C02 startsnp=variant.11821 endsnp=rs2488140 conf=10.270
chr11:58803621-58834900 numsnp=4 length=31,280 state5,cn=3 3999899096_R09C02 startsnp=rs3740952 endsnp=rs563191 conf=6.092
chr12:9658741-9723763 numsnp=8 length=65,023 state5,cn=3 3999899096_R09C02 startsnp=psy_rs10843924 endsnp=psy_rs77247953 conf=10.270
chr12:66516450-66517700 numsnp=3 length=1,251 state5,cn=3 3999899096_R09C02 startsnp=rs35447479 endsnp=indel.25841 conf=2.918
chr18:5945376-5949720 numsnp=3 length=4,345 state5,cn=3 3999899096_R09C02 startsnp=rs11662696 endsnp=psy_rs9947546 conf=4.770
chr20:15031044-15054436 numsnp=5 length=23,393 state5,cn=3 3999899096_R09C02 startsnp=rs6110505 endsnp=rs415134 conf=8.832
chr1:243803714-243813097 numsnp=3 length=9,384 state1,cn=0 3999899142_R02C01 startsnp=psy_rs1486472 endsnp=psy_rs77030218 conf=7.250
chr2:194691051-194694686 numsnp=3 length=3,636 state1,cn=0 3999899142_R02C01 startsnp=psy_rs73984715 endsnp=psy_rs12987240 conf=6.008
chr3:16926648-16926699 numsnp=3 length=52 state1,cn=0 3999899142_R02C01 startsnp=exm294561 endsnp=exm294563 conf=6.259
chr3:51990315-51990763 numsnp=4 length=449 state1,cn=0 3999899142_R02C01 startsnp=exm319549 endsnp=exm319565 conf=6.302
chr19:58867567-58868480 numsnp=5 length=914 state1,cn=0 3999899142_R02C01 startsnp=exm1516408 endsnp=exm1516459 conf=6.453
chr20:60988951-60989187 numsnp=5 length=237 state1,cn=0 3999899142_R02C01 startsnp=exm1556510 endsnp=exm1556527 conf=11.424
chr22:50228087-50239154 numsnp=6 length=11,068 state1,cn=0 3999899142_R02C01 startsnp=psy_rs138892 endsnp=psy_rs11704466 conf=12.039
chr1:10708142-10713980 numsnp=8 length=5,839 state2,cn=1 3999899142_R02C01 startsnp=rs778228 endsnp=exm1690697 conf=17.242
chr2:95976119-95977790 numsnp=4 length=1,672 state2,cn=1 3999899142_R02C01 startsnp=exm212035 endsnp=rs889852 conf=10.532
chr7:41072834-41101298 numsnp=4 length=28,465 state2,cn=1 3999899142_R02C01 startsnp=exm2266398 endsnp=psy_rs112156721 conf=10.878
chr10:135081558-135095750 numsnp=28 length=14,193 state2,cn=1 3999899142_R02C01 startsnp=exm867889 endsnp=exm868097 conf=19.211
chr14:103392249-103396961 numsnp=6 length=4,713 state2,cn=1 3999899142_R02C01 startsnp=rs1190229 endsnp=exm1129346 conf=18.126
chr1:13171847-13187294 numsnp=8 length=15,448 state5,cn=3 3999899142_R02C01 startsnp=kgp11050191 endsnp=kgp3971131 conf=12.629
chr13:99126303-99358478 numsnp=57 length=232,176 state5,cn=3 3999899142_R02C01 startsnp=exm-rs9517320 endsnp=rs8187836 conf=90.723
chr13:101527030-101804227 numsnp=85 length=277,198 state5,cn=3 3999899142_R02C01 startsnp=rs666201 endsnp=rs9554756 conf=81.596
chr18:2361995-2407726 numsnp=5 length=45,732 state5,cn=3 3999899142_R02C01 startsnp=rs7232532 endsnp=psy_rs7226758 conf=7.505
chr19:19868879-19911700 numsnp=13 length=42,822 state5,cn=3 3999899142_R02C01 startsnp=rs247782 endsnp=psy_rs117660826 conf=14.777
chrX:3013032-3019935 numsnp=5 length=6,904 state1,cn=0 3999899142_R02C01 startsnp=rs1454500 endsnp=snv-rs111280082 conf=25.057
chrX:27413802-27435308 numsnp=3 length=21,507 state1,cn=0 3999899142_R02C01 startsnp=snv-rs192808150 endsnp=rs2379024 conf=8.681
chrX:88996555-89104765 numsnp=5 length=108,211 state1,cn=0 3999899142_R02C01 startsnp=rs2987881 endsnp=exm2263170 conf=10.726
chrX:89662079-89824761 numsnp=7 length=162,683 state1,cn=0 3999899142_R02C01 startsnp=kgp22803046 endsnp=rs2755514 conf=1.916
chrX:990180-1216188 numsnp=4 length=226,009 state3,cn=2 3999899142_R02C01 startsnp=exm-rs4129148 endsnp=kgp30790682 conf=3.861
chrX:2209590-2233693 numsnp=3 length=24,104 state3,cn=2 3999899142_R02C01 startsnp=exm1625610 endsnp=kgp22770430 conf=7.300
chr4:173426583-173429510 numsnp=3 length=2,928 state1,cn=0 3999899142_R08C01 startsnp=psy_rs7693645 endsnp=psy_rs112429191 conf=8.609
chr6:57587550-57620876 numsnp=3 length=33,327 state1,cn=0 3999899142_R08C01 startsnp=psy_rs146333445 endsnp=psy_rs145112474 conf=9.793
chr11:130848830-130866090 numsnp=7 length=17,261 state1,cn=0 3999899142_R08C01 startsnp=psy_rs61909204 endsnp=psy_rs961491 conf=13.903
chr22:50228087-50239154 numsnp=6 length=11,068 state1,cn=0 3999899142_R08C01 startsnp=psy_rs138892 endsnp=psy_rs11704466 conf=21.730
chr3:10219555-10220830 numsnp=6 length=1,276 state2,cn=1 3999899142_R08C01 startsnp=exm289680 endsnp=rs17610830 conf=13.340
chr15:30919043-31088443 numsnp=12 length=169,401 state2,cn=1 3999899142_R08C01 startsnp=exm1144363 endsnp=rs798139 conf=25.363
chr15:34727994-34800595 numsnp=5 length=72,602 state2,cn=1 3999899142_R08C01 startsnp=psy_rs79184910 endsnp=rs4924714 conf=12.886
chr1:110230278-110233147 numsnp=5 length=2,870 state5,cn=3 3999899142_R08C01 startsnp=psy_rs36208869 endsnp=exm-rs1056806 conf=1.818
chr12:75889428-75925776 numsnp=18 length=36,349 state5,cn=3 3999899142_R08C01 startsnp=exm1022683 endsnp=rs10879928 conf=17.657
chr12:133046268-133046915 numsnp=4 length=648 state5,cn=3 3999899142_R08C01 startsnp=psy_rs12228614 endsnp=psy_rs4883588 conf=0.399
chr14:77102150-77112202 numsnp=3 length=10,053 state5,cn=3 3999899142_R08C01 startsnp=psy_rs1642839 endsnp=rs1625024 conf=5.489
chr14:106067618-106127330 numsnp=5 length=59,713 state5,cn=3 3999899142_R08C01 startsnp=rs12884681 endsnp=kgp4991126 conf=10.071
chr18:13731520-13732454 numsnp=9 length=935 state5,cn=3 3999899142_R08C01 startsnp=exm1376929 endsnp=rs8096764 conf=11.413
chr22:25753777-25917686 numsnp=28 length=163,910 state5,cn=3 3999899142_R08C01 startsnp=rs5996921 endsnp=psy_rs5761100 conf=26.037
chrX:1314931-1325361 numsnp=9 length=10,431 state2,cn=1 3999899142_R08C01 startsnp=exm1624783 endsnp=exm2248602 conf=10.197
chrX:79325880-79356035 numsnp=5 length=30,156 state5,cn=3 3999899142_R08C01 startsnp=rs74948985 endsnp=rs6621690 conf=2.019
chr2:194691051-194694686 numsnp=3 length=3,636 state1,cn=0 9464294016_R01C02 startsnp=psy_rs73984715 endsnp=psy_rs12987240 conf=11.070
chr4:173426583-173429510 numsnp=3 length=2,928 state1,cn=0 9464294016_R01C02 startsnp=psy_rs7693645 endsnp=psy_rs112429191 conf=13.424
chr1:92579206-92595338 numsnp=3 length=16,133 state2,cn=1 9464294016_R01C02 startsnp=rs1226187 endsnp=var_1_92595338 conf=12.514
chr2:210000798-210024938 numsnp=5 length=24,141 state2,cn=1 9464294016_R01C02 startsnp=rs2886188 endsnp=rs7587994 conf=27.356
chr4:172870885-172880449 numsnp=4 length=9,565 state2,cn=1 9464294016_R01C02 startsnp=rs6553603 endsnp=rs332969 conf=19.687
chr5:49537784-49554249 numsnp=7 length=16,466 state2,cn=1 9464294016_R01C02 startsnp=psy_rs497656 endsnp=psy_rs4865670 conf=15.539
chr5:120178687-120280194 numsnp=8 length=101,508 state2,cn=1 9464294016_R01C02 startsnp=rs11958476 endsnp=rs2909938 conf=36.802
chr15:20161372-20192086 numsnp=7 length=30,715 state2,cn=1 9464294016_R01C02 startsnp=rs6599770 endsnp=rs4932078 conf=35.256
chr17:44332093-44363740 numsnp=5 length=31,648 state2,cn=1 9464294016_R01C02 startsnp=psy_rs143613166 endsnp=psy_rs145095061 conf=13.580
chr1:13171847-13374928 numsnp=9 length=203,082 state5,cn=3 9464294016_R01C02 startsnp=kgp11050191 endsnp=kgp6897585 conf=20.280
chr2:242758176-242758301 numsnp=4 length=126 state5,cn=3 9464294016_R01C02 startsnp=exm285235 endsnp=exm285249 conf=10.502
chr5:685748-796664 numsnp=8 length=110,917 state5,cn=3 9464294016_R01C02 startsnp=rs386057 endsnp=psy_rs138932630 conf=19.973
chr5:139931633-139931650 numsnp=9 length=18 state5,cn=3 9464294016_R01C02 startsnp=exm2088587 endsnp=exm482444 conf=24.406
chr10:47541708-47703946 numsnp=35 length=162,239 state5,cn=3 9464294016_R01C02 startsnp=psy_rs74622866 endsnp=kgp3883096 conf=100.168
chr11:5906048-5922222 numsnp=16 length=16,175 state5,cn=3 9464294016_R01C02 startsnp=exm884138 endsnp=rs10160336 conf=44.022
chr12:133046268-133046915 numsnp=4 length=648 state5,cn=3 9464294016_R01C02 startsnp=psy_rs12228614 endsnp=psy_rs4883588 conf=0.000
chr16:28618318-28621318 numsnp=7 length=3,001 state5,cn=3 9464294016_R01C02 startsnp=rs1042014 endsnp=kgp16473159 conf=17.574
chr22:24287786-24302480 numsnp=5 length=14,695 state5,cn=3 9464294016_R01C02 startsnp=psy_rs180865854 endsnp=psy_rs181983734 conf=13.474
chr4:173426583-173429510 numsnp=3 length=2,928 state1,cn=0 9464294016_R02C01 startsnp=psy_rs7693645 endsnp=psy_rs112429191 conf=7.909
chr5:17726288-17775057 numsnp=12 length=48,770 state2,cn=1 9464294016_R02C01 startsnp=psy_rs35207789 endsnp=psy_rs77423390 conf=52.721
chr6:26370616-26428223 numsnp=51 length=57,608 state2,cn=1 9464294016_R02C01 startsnp=exm2264221 endsnp=newrs189780701 conf=112.739
chr10:68336295-68353739 numsnp=5 length=17,445 state2,cn=1 9464294016_R02C01 startsnp=rs10997242 endsnp=rs1911338 conf=17.774
chr11:48773217-48819284 numsnp=4 length=46,068 state2,cn=1 9464294016_R02C01 startsnp=psy_rs138628568 endsnp=psy_rs149805194 conf=11.273
chr14:42782876-43030843 numsnp=25 length=247,968 state2,cn=1 9464294016_R02C01 startsnp=rs2626432 endsnp=rs7156273 conf=105.819
chr1:976963-977396 numsnp=4 length=434 state5,cn=3 9464294016_R02C01 startsnp=exm988 endsnp=exm1002 conf=8.739
chr1:1222958-1226912 numsnp=26 length=3,955 state5,cn=3 9464294016_R02C01 startsnp=exm2153 endsnp=exm2272 conf=45.415
chr1:10709453-10709469 numsnp=3 length=17 state5,cn=3 9464294016_R02C01 startsnp=exm13552 endsnp=exm1690682 conf=3.361
chr2:167137002-167137100 numsnp=19 length=99 state5,cn=3 9464294016_R02C01 startsnp=chr2_167137002 endsnp=chr2_167137100 conf=34.173
chr2:241398543-241401986 numsnp=11 length=3,444 state5,cn=3 9464294016_R02C01 startsnp=exm281741 endsnp=exm281778 conf=14.442
chr2:241835039-241835543 numsnp=7 length=505 state5,cn=3 9464294016_R02C01 startsnp=exm283087 endsnp=rs10206101 conf=17.921
chr2:242752763-242758301 numsnp=17 length=5,539 state5,cn=3 9464294016_R02C01 startsnp=rs760133 endsnp=exm285249 conf=15.266
chr4:981602-984948 numsnp=28 length=3,347 state5,cn=3 9464294016_R02C01 startsnp=exm379966 endsnp=exm380092 conf=30.897
chr4:8229105-8230456 numsnp=18 length=1,352 state5,cn=3 9464294016_R02C01 startsnp=exm388247 endsnp=rs1281152 conf=18.294
chr5:814875-825329 numsnp=12 length=10,455 state5,cn=3 9464294016_R02C01 startsnp=exm440971 endsnp=exm441004 conf=20.880
chr7:2577871-2579497 numsnp=18 length=1,627 state5,cn=3 9464294016_R02C01 startsnp=exm599839 endsnp=exm599923 conf=22.394
chr7:76637441-76639871 numsnp=3 length=2,431 state5,cn=3 9464294016_R02C01 startsnp=rs10278476 endsnp=kgp5649021 conf=11.333
chr8:7308356-7308718 numsnp=5 length=363 state5,cn=3 9464294016_R02C01 startsnp=indel.99556 endsnp=exm679908 conf=9.388
chr8:144681397-144687901 numsnp=8 length=6,505 state5,cn=3 9464294016_R02C01 startsnp=exm727234 endsnp=exm727259 conf=15.275
chr8:144943745-144946345 numsnp=32 length=2,601 state5,cn=3 9464294016_R02C01 startsnp=exm728748 endsnp=psy_rs34753358 conf=39.758
chr9:140093696-140094273 numsnp=10 length=578 state5,cn=3 9464294016_R02C01 startsnp=exm802270 endsnp=exm802303 conf=17.863
chr9:140173637-140196334 numsnp=6 length=22,698 state5,cn=3 9464294016_R02C01 startsnp=exm803057 endsnp=exm803109 conf=13.291
chr10:135012384-135032385 numsnp=19 length=20,002 state5,cn=3 9464294016_R02C01 startsnp=exm2216909 endsnp=variant.15372 conf=20.104
chr10:135080873-135089077 numsnp=26 length=8,205 state5,cn=3 9464294016_R02C01 startsnp=exm867880 endsnp=exm868076 conf=23.907
chr11:284297-290913 numsnp=18 length=6,617 state5,cn=3 9464294016_R02C01 startsnp=exm869817 endsnp=exm869893 conf=20.667
chr12:132401542-132405765 numsnp=12 length=4,224 state5,cn=3 9464294016_R02C01 startsnp=exm1052332 endsnp=exm1052408 conf=17.013
chr15:42175564-42178519 numsnp=12 length=2,956 state5,cn=3 9464294016_R02C01 startsnp=exm1152805 endsnp=exm1152837 conf=20.900
chr16:675680-683905 numsnp=12 length=8,226 state5,cn=3 9464294016_R02C01 startsnp=exm-rs763014 endsnp=exm1197392 conf=21.648
chr16:1270317-1270935 numsnp=25 length=619 state5,cn=3 9464294016_R02C01 startsnp=chr16_1270317 endsnp=chr16_1270935 conf=37.793
chr16:2140680-2147338 numsnp=20 length=6,659 state5,cn=3 9464294016_R02C01 startsnp=exm1205480 endsnp=exm1205597 conf=19.019
chr16:88570383-88601281 numsnp=14 length=30,899 state5,cn=3 9464294016_R02C01 startsnp=rs868874 endsnp=exm1267924 conf=14.239
chr17:79094122-79096115 numsnp=14 length=1,994 state5,cn=3 9464294016_R02C01 startsnp=exm1365383 endsnp=exm1365488 conf=24.110
chr17:79425367-79429005 numsnp=21 length=3,639 state5,cn=3 9464294016_R02C01 startsnp=exm1366596 endsnp=exm1366742 conf=29.533
chr17:80048271-80049206 numsnp=10 length=936 state5,cn=3 9464294016_R02C01 startsnp=exm1369369 endsnp=exm1369401 conf=16.696
chr20:60891045-60892813 numsnp=14 length=1,769 state5,cn=3 9464294016_R02C01 startsnp=exm1555652 endsnp=exm1555702 conf=28.440
chr20:62195426-62200204 numsnp=56 length=4,779 state5,cn=3 9464294016_R02C01 startsnp=exm1972360 endsnp=exm1559809 conf=30.492
chr21:47558501-47558559 numsnp=6 length=59 state5,cn=3 9464294016_R02C01 startsnp=exm1580750 endsnp=exm1580759 conf=11.380
chr22:50942805-50943101 numsnp=8 length=297 state5,cn=3 9464294016_R02C01 startsnp=exm1623108 endsnp=exm1623134 conf=20.160
chr2:194691051-194694686 numsnp=3 length=3,636 state1,cn=0 9464294016_R03C01 startsnp=psy_rs73984715 endsnp=psy_rs12987240 conf=7.425
chr12:9703054-9723763 numsnp=4 length=20,710 state1,cn=0 9464294016_R03C01 startsnp=psy_rs10843999 endsnp=psy_rs77247953 conf=6.616
chr22:50228087-50239154 numsnp=6 length=11,068 state1,cn=0 9464294016_R03C01 startsnp=psy_rs138892 endsnp=psy_rs11704466 conf=13.827
chr4:17546381-17561139 numsnp=3 length=14,759 state2,cn=1 9464294016_R03C01 startsnp=rs6843189 endsnp=rs6828925 conf=15.792
chr5:49511425-49538829 numsnp=8 length=27,405 state2,cn=1 9464294016_R03C01 startsnp=psy_rs8188088 endsnp=psy_rs577482 conf=15.998
chr6:31219869-31221914 numsnp=4 length=2,046 state2,cn=1 9464294016_R03C01 startsnp=rs9264179 endsnp=rs9264219 conf=18.167
chr7:15063833-15100749 numsnp=12 length=36,917 state2,cn=1 9464294016_R03C01 startsnp=exm-rs10244051 endsnp=rs17348054 conf=60.253
chr10:58916759-58936553 numsnp=4 length=19,795 state2,cn=1 9464294016_R03C01 startsnp=rs6481254 endsnp=rs7081958 conf=16.032
chr19:20630360-20716939 numsnp=9 length=86,580 state2,cn=1 9464294016_R03C01 startsnp=rs10408291 endsnp=psy_rs78893254 conf=24.836
chr22:39428305-39445554 numsnp=7 length=17,250 state2,cn=1 9464294016_R03C01 startsnp=exm1609339 endsnp=rs2076101 conf=18.107
chr1:752566-846808 numsnp=6 length=94,243 state5,cn=3 9464294016_R03C01 startsnp=rs3094315 endsnp=rs4475691 conf=24.455
chr1:1222895-1226889 numsnp=25 length=3,995 state5,cn=3 9464294016_R03C01 startsnp=exm2144 endsnp=exm2270 conf=22.814
chr1:110215178-110233147 numsnp=6 length=17,970 state5,cn=3 9464294016_R03C01 startsnp=rs655315 endsnp=exm-rs1056806 conf=14.110
chr2:98235080-98238538 numsnp=3 length=3,459 state5,cn=3 9464294016_R03C01 startsnp=psy_rs2692943 endsnp=psy_rs2922532 conf=14.707
chr5:139931633-139936825 numsnp=22 length=5,193 state5,cn=3 9464294016_R03C01 startsnp=exm2088587 endsnp=exm482478 conf=23.716
chr7:44935-62643 numsnp=5 length=17,709 state5,cn=3 9464294016_R03C01 startsnp=rs7456436 endsnp=rs9642256 conf=22.146
chr7:49050763-49071509 numsnp=4 length=20,747 state5,cn=3 9464294016_R03C01 startsnp=rs4256549 endsnp=rs7804817 conf=16.726
chr8:144877618-144886308 numsnp=12 length=8,691 state5,cn=3 9464294016_R03C01 startsnp=exm728035 endsnp=exm728080 conf=19.971
chr10:26922969-26993080 numsnp=12 length=70,112 state5,cn=3 9464294016_R03C01 startsnp=psy_rs61012955 endsnp=rs11015236 conf=49.469
chr10:27044667-27258640 numsnp=35 length=213,974 state5,cn=3 9464294016_R03C01 startsnp=exm815898 endsnp=rs7069690 conf=143.083
chr10:27454316-27586972 numsnp=61 length=132,657 state5,cn=3 9464294016_R03C01 startsnp=exm816306 endsnp=rs11015657 conf=119.995
chr17:34442465-34477887 numsnp=13 length=35,423 state5,cn=3 9464294016_R03C01 startsnp=psy_rs148431271 endsnp=rs4796168 conf=26.112
chr17:80541944-80545133 numsnp=22 length=3,190 state5,cn=3 9464294016_R03C01 startsnp=exm1370410 endsnp=exm1370489 conf=25.826
chr20:62194464-62196253 numsnp=20 length=1,790 state5,cn=3 9464294016_R03C01 startsnp=exm1972354 endsnp=exm1559627 conf=27.989
chrX:34432433-34449197 numsnp=3 length=16,765 state5,cn=3 9464294016_R03C01 startsnp=rs5973188 endsnp=rs4829149 conf=3.022
chrX:35873056-35941529 numsnp=9 length=68,474 state5,cn=3 9464294016_R03C01 startsnp=rs2336401 endsnp=rs13440948 conf=12.216
chrX:36007464-36007614 numsnp=3 length=151 state5,cn=3 9464294016_R03C01 startsnp=exm1633910 endsnp=rs6629027 conf=0.905
chrX:37526542-37529705 numsnp=5 length=3,164 state5,cn=3 9464294016_R03C01 startsnp=indel.107919 endsnp=kgp22779346 conf=7.238
chr4:173426583-173429510 numsnp=3 length=2,928 state1,cn=0 9464294016_R03C02 startsnp=psy_rs7693645 endsnp=psy_rs112429191 conf=8.576
chr22:50228087-50239154 numsnp=6 length=11,068 state1,cn=0 9464294016_R03C02 startsnp=psy_rs138892 endsnp=psy_rs11704466 conf=10.744
chr1:213005012-213011812 numsnp=9 length=6,801 state2,cn=1 9464294016_R03C02 startsnp=rs6694190 endsnp=rs7524203 conf=37.457
chr12:133046268-133046915 numsnp=4 length=648 state2,cn=1 9464294016_R03C02 startsnp=psy_rs12228614 endsnp=psy_rs4883588 conf=9.474
chr14:22694672-22694963 numsnp=4 length=292 state2,cn=1 9464294016_R03C02 startsnp=variant.30917 endsnp=variant.30920 conf=16.376
chr14:44507151-44519214 numsnp=4 length=12,064 state2,cn=1 9464294016_R03C02 startsnp=rs1955970 endsnp=rs6572235 conf=20.696
chr15:20161372-20192086 numsnp=7 length=30,715 state2,cn=1 9464294016_R03C02 startsnp=rs6599770 endsnp=rs4932078 conf=25.738
chr2:98235080-98238538 numsnp=3 length=3,459 state5,cn=3 9464294016_R03C02 startsnp=psy_rs2692943 endsnp=psy_rs2922532 conf=13.779
chr4:161861640-161927775 numsnp=7 length=66,136 state5,cn=3 9464294016_R03C02 startsnp=rs7436001 endsnp=psy_rs80120634 conf=28.311
chr5:139931633-139931740 numsnp=20 length=108 state5,cn=3 9464294016_R03C02 startsnp=exm2088587 endsnp=exm482463 conf=25.968
chr11:5906073-5908939 numsnp=13 length=2,867 state5,cn=3 9464294016_R03C02 startsnp=exm884139 endsnp=rs1453433 conf=35.339
chr12:7995643-8083081 numsnp=19 length=87,439 state5,cn=3 9464294016_R03C02 startsnp=psy_rs146408584 endsnp=exm981267 conf=65.156
chr20:62190628-62191475 numsnp=10 length=848 state5,cn=3 9464294016_R03C02 startsnp=exm1559350 endsnp=psy_rs3810478 conf=25.591
chr20:62326538-62328428 numsnp=8 length=1,891 state5,cn=3 9464294016_R03C02 startsnp=exm1560323 endsnp=exm1560386 conf=19.869
chrX:134947910-134947990 numsnp=3 length=81 state1,cn=0 9464294016_R03C02 startsnp=exm1658595 endsnp=exm1658607 conf=23.878
chr1:12849870-12854507 numsnp=3 length=4,638 state1,cn=0 9464294016_R05C02 startsnp=psy_rs11583964 endsnp=exm17235 conf=11.255
chr1:12919838-12921156 numsnp=11 length=1,319 state1,cn=0 9464294016_R05C02 startsnp=exm17540 endsnp=exm17593 conf=56.916
chr1:12921272-12921311 numsnp=3 length=40 state1,cn=0 9464294016_R05C02 startsnp=exm17609 endsnp=exm17613 conf=6.054
chr4:173426583-173429510 numsnp=3 length=2,928 state1,cn=0 9464294016_R05C02 startsnp=psy_rs7693645 endsnp=psy_rs112429191 conf=13.796
chr22:50228087-50239154 numsnp=6 length=11,068 state1,cn=0 9464294016_R05C02 startsnp=psy_rs138892 endsnp=psy_rs11704466 conf=7.971
chr1:12866590-12866899 numsnp=3 length=310 state2,cn=1 9464294016_R05C02 startsnp=rs848428 endsnp=rs9308457 conf=16.444
chr1:12907683-12919111 numsnp=7 length=11,429 state2,cn=1 9464294016_R05C02 startsnp=exm17419 endsnp=exm17499 conf=11.994
chr1:12921246-12921255 numsnp=4 length=10 state2,cn=1 9464294016_R05C02 startsnp=exm17603 endsnp=exm17606 conf=10.803
chr1:213005012-213011812 numsnp=9 length=6,801 state2,cn=1 9464294016_R05C02 startsnp=rs6694190 endsnp=rs7524203 conf=37.681
chr1:242059221-242064633 numsnp=4 length=5,413 state2,cn=1 9464294016_R05C02 startsnp=rs4658535 endsnp=rs7551606 conf=7.211
chr2:243020723-243048760 numsnp=3 length=28,038 state2,cn=1 9464294016_R05C02 startsnp=rs4973686 endsnp=rs12478296 conf=13.774
chr5:46345089-46362346 numsnp=15 length=17,258 state2,cn=1 9464294016_R05C02 startsnp=psy_rs35335986 endsnp=psy_rs11949371 conf=16.252
chr11:67501626-67594702 numsnp=9 length=93,077 state2,cn=1 9464294016_R05C02 startsnp=rs10791923 endsnp=kgp4770289 conf=32.658
chr11:81509575-81516733 numsnp=4 length=7,159 state2,cn=1 9464294016_R05C02 startsnp=rs1542465 endsnp=rs11232877 conf=16.049
chr15:20161372-20192086 numsnp=7 length=30,715 state2,cn=1 9464294016_R05C02 startsnp=rs6599770 endsnp=rs4932078 conf=38.538
chr1:161492587-161512848 numsnp=6 length=20,262 state5,cn=3 9464294016_R05C02 startsnp=rs12129787 endsnp=exm118068 conf=17.425
chr2:98235080-98238538 numsnp=3 length=3,459 state5,cn=3 9464294016_R05C02 startsnp=psy_rs2692943 endsnp=psy_rs2922532 conf=12.595
chr4:145009802-145038131 numsnp=8 length=28,330 state5,cn=3 9464294016_R05C02 startsnp=rs7657795 endsnp=variant.82937 conf=28.468
chr9:135951231-135962478 numsnp=3 length=11,248 state5,cn=3 9464294016_R05C02 startsnp=rs2283134 endsnp=psy_rs62576805 conf=10.887
chr10:11805412-11805494 numsnp=4 length=83 state5,cn=3 9464294016_R05C02 startsnp=exm809375 endsnp=exm809385 conf=11.177
chr17:34442465-34477887 numsnp=13 length=35,423 state5,cn=3 9464294016_R05C02 startsnp=psy_rs148431271 endsnp=rs4796168 conf=18.362
chr21:47558501-47558559 numsnp=6 length=59 state5,cn=3 9464294016_R05C02 startsnp=exm1580750 endsnp=exm1580759 conf=15.282
chrX:1216188-1558028 numsnp=61 length=341,841 state2,cn=1 9464294016_R05C02 startsnp=kgp30790682 endsnp=exm1625277 conf=13.396
chrX:2139168-2233693 numsnp=8 length=94,526 state2,cn=1 9464294016_R05C02 startsnp=exm1625569 endsnp=kgp22770430 conf=10.507
chrX:23552489-23571087 numsnp=4 length=18,599 state5,cn=3 9464294016_R05C02 startsnp=rs5925823 endsnp=rs6629682 conf=7.334
chrX:34432433-34449197 numsnp=3 length=16,765 state5,cn=3 9464294016_R05C02 startsnp=rs5973188 endsnp=rs4829149 conf=2.757
chrX:42476601-42522632 numsnp=4 length=46,032 state5,cn=3 9464294016_R05C02 startsnp=rs4827306 endsnp=snv-rs112794456 conf=4.375
chrX:149005063-149013963 numsnp=8 length=8,901 state5,cn=3 9464294016_R05C02 startsnp=rs2166782 endsnp=exm1661492 conf=3.655
chrX:153037394-153041544 numsnp=13 length=4,151 state5,cn=3 9464294016_R05C02 startsnp=exm1664088 endsnp=rs5987155 conf=9.654
chr2:194691051-194694686 numsnp=3 length=3,636 state1,cn=0 9464294016_R07C02 startsnp=psy_rs73984715 endsnp=psy_rs12987240 conf=9.060
chr4:173426583-173429510 numsnp=3 length=2,928 state1,cn=0 9464294016_R07C02 startsnp=psy_rs7693645 endsnp=psy_rs112429191 conf=8.197
chr8:39284717-39321992 numsnp=4 length=37,276 state1,cn=0 9464294016_R07C02 startsnp=psy_rs7827037 endsnp=psy_rs28851014 conf=21.822
chr2:225244304-225244923 numsnp=5 length=620 state2,cn=1 9464294016_R07C02 startsnp=variant.65840 endsnp=rs3738953 conf=19.671
chr5:139931607-139931656 numsnp=21 length=50 state2,cn=1 9464294016_R07C02 startsnp=exm482409 endsnp=exm482450 conf=36.081
chr8:24207409-24207472 numsnp=5 length=64 state2,cn=1 9464294016_R07C02 startsnp=exm690047 endsnp=exm690053 conf=19.841
chr9:11976830-11996831 numsnp=3 length=20,002 state2,cn=1 9464294016_R07C02 startsnp=rs16928298 endsnp=rs4512479 conf=12.814
chr16:72089740-72108264 numsnp=13 length=18,525 state2,cn=1 9464294016_R07C02 startsnp=rs2070937 endsnp=exm1256782 conf=14.001
chr19:20596024-20716939 numsnp=11 length=120,916 state2,cn=1 9464294016_R07C02 startsnp=psy_rs6511102 endsnp=psy_rs78893254 conf=26.229
chr1:1222596-1249194 numsnp=64 length=26,599 state5,cn=3 9464294016_R07C02 startsnp=exm2135 endsnp=indel.166 conf=30.720
chr1:3389703-3416502 numsnp=38 length=26,800 state5,cn=3 9464294016_R07C02 startsnp=exm6750 endsnp=psy_rs41307852 conf=29.808
chr2:98235080-98242427 numsnp=4 length=7,348 state5,cn=3 9464294016_R07C02 startsnp=psy_rs2692943 endsnp=kgp1336864 conf=14.091
chr2:239038829-239040270 numsnp=16 length
|
|
Generally you need to compile PFB from at least 100 samples, the more the
better. You may want to request the original PFB files to re-generate
results. Additionally, the LOG message should tell you how many markers are
used in the calculation, since it is possible that only a fraction of
markers in your input files are actually used (based on PFB file).
Not sure what is the gcmodel file that you used, but it is usually not
needed to use a gcmodel unless there are clear problems with the LRR
calculation (large WF values).
I do not think the version of PennCNV itself can change results much, and
the hhall.hmm has not changed either.
…On Sat, Jan 2, 2021 at 11:42 AM Qidi Feng ***@***.***> wrote:
Hi Kai,
Thank you very much for your reply! But now I got problems repeating
previous paper's calling results with almost the same pipeline. Would you
pls give me any hints?
The previous paper claims that they use "“hhall.hmm”, compile pfb from the
data, use gcmodel adjustment, using an older version of PennCNV
v2010May01". I connected with the author and got their inputs of 100
samples (containing BAF and LRR), I run PennCNVv1.0.5 with command "perl
detect_cnv.pl -test -hmm ../PennCNV-1.0.5/lib/hhall.hmm -pfb taiwan100.pfb
-gcmodel taiwan100.gc2 -listfile samplelist.txt -log rawcnv.log -out
taiwan100.rawcnv". I compared their raw cnv results with mine, and found
there are big differences in number of CNVs for some specific samples (for
example 9464294022_R03C01). You may like to check detailed results between
the two versions of results in the attached file.
The only difference in pipeline I can think of is 1. pfb file (I compiled
pfb file from the 100 samples while the previous paper should compile pfb
file from the original ~5000 samples) and 2. PennCNV version. Do you have
any suggestions explaining the differences on cnv results? Do you think PFB
file could potentially cause this difference?
Thanks again for your help! Happy new year!
Best,
Qidi
On Sat, Jan 2, 2021 at 12:13 AM Kai Wang ***@***.***> wrote:
> PennCNV is not in github around 2010 (This is not v1.0.0). I do not have
a
> copy of the 2010 version at hand; however, I believe that very minimal
> changes are made to PennCNV CNV calling procedure itself (most changes
are
> for accessary programs, and for processing outputs or for increasing
> compatibility with non-human species). I think you can just use the
latest
> version to do CNV calling.
>
> On Fri, Jan 1, 2021 at 11:18 AM Qidi Feng ***@***.***>
> wrote:
>
> > Hi Kai,
> >
> > I am trying to use the same PennCNV version with a previously published
> > paper in order to make the cnv results more comparable? The PennCNV
used
> in
> > that paper is PennCNV v2010May01. I am not sure which version is this?
Is
> > this PennCNV v1.0.0?
> >
> > Happy new year!
> >
> > Best regards,
> > Qidi Feng
> >
> > —
> > You are receiving this because you are subscribed to this thread.
> > Reply to this email directly, view it on GitHub
> > <#64>, or unsubscribe
> > <
>
https://github.com/notifications/unsubscribe-auth/ABNG3OETC4OKB7KGZQWUSBLSXXYTZANCNFSM4VQLXVFQ
> >
> > .
> >
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
> <#64 (comment)>, or
> unsubscribe
> <
https://github.com/notifications/unsubscribe-auth/AJ6PSOGY7MLVNYH6O5YRNVTSX2TPDANCNFSM4VQLXVFQ
>
> .
>
chr6:57587550-57620876 numsnp=3 length=33,327 state1,cn=0
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chr7:70419818-70422360 numsnp=3 length=2,543 state1,cn=0 3999879003_R02C01
startsnp=rs1464853 endsnp=psy_rs60233550 conf=9.012
chr16:3613019-3613263 numsnp=5 length=245 state1,cn=0 3999879003_R02C01
startsnp=exm1211533 endsnp=exm1211547 conf=14.304
chr16:70045749-70089450 numsnp=3 length=43,702 state1,cn=0
3999879003_R02C01 startsnp=psy_rs11648231 endsnp=psy_rs150266884 conf=6.804
chr5:70307162-70308607 numsnp=9 length=1,446 state2,cn=1 3999879003_R02C01
startsnp=exm459256 endsnp=variant.85123 conf=8.043
chr15:84700097-84706544 numsnp=14 length=6,448 state2,cn=1
3999879003_R02C01 startsnp=exm1184260 endsnp=exm1184280 conf=29.454
chr21:37107446-37195391 numsnp=8 length=87,946 state2,cn=1
3999879003_R02C01 startsnp=rs2835109 endsnp=rs2222963 conf=17.425
chr1:12919081-13187294 numsnp=29 length=268,214 state5,cn=3
3999879003_R02C01 startsnp=exm17491 endsnp=kgp3971131 conf=31.216
chr1:97735667-97757424 numsnp=5 length=21,758 state5,cn=3
3999879003_R02C01 startsnp=rs1520668 endsnp=rs10465748 conf=3.974
chr1:117983815-117989275 numsnp=3 length=5,461 state5,cn=3
3999879003_R02C01 startsnp=rs10923297 endsnp=rs4659050 conf=4.682
chr2:20096767-20113967 numsnp=15 length=17,201 state5,cn=3
3999879003_R02C01 startsnp=exm174761 endsnp=exm174823 conf=6.807
chr2:39278400-39305489 numsnp=11 length=27,090 state5,cn=3
3999879003_R02C01 startsnp=exm188386 endsnp=rs297136 conf=12.072
chr2:55539905-55573401 numsnp=18 length=33,497 state5,cn=3
3999879003_R02C01 startsnp=rs10189439 endsnp=exm195158 conf=15.472
chr2:61472345-61508231 numsnp=14 length=35,887 state5,cn=3
3999879003_R02C01 startsnp=exm196534 endsnp=exm2255436 conf=7.958
chr2:62193438-62235524 numsnp=5 length=42,087 state5,cn=3
3999879003_R02C01 startsnp=rs11677744 endsnp=psy_rs5019426 conf=6.815
chr2:145463764-145540283 numsnp=6 length=76,520 state5,cn=3
3999879003_R02C01 startsnp=rs2195114 endsnp=psy_rs144473890 conf=4.952
chr2:154058372-154173881 numsnp=14 length=115,510 state5,cn=3
3999879003_R02C01 startsnp=rs4664649 endsnp=rs13021542 conf=13.340
chr3:155539266-155560337 numsnp=8 length=21,072 state5,cn=3
3999879003_R02C01 startsnp=rs11921267 endsnp=exm2042129 conf=0.000
chr3:160119716-160143943 numsnp=26 length=24,228 state5,cn=3
3999879003_R02C01 startsnp=newrs141089654 endsnp=exm361926 conf=13.113
chr3:188112554-188116784 numsnp=3 length=4,231 state5,cn=3
3999879003_R02C01 startsnp=exm-rs1464510 endsnp=rs9820681 conf=0.000
chr4:221623-266171 numsnp=13 length=44,549 state5,cn=3 3999879003_R02C01
startsnp=rs7695945 endsnp=exm378389 conf=8.974
chr4:410015-442021 numsnp=27 length=32,007 state5,cn=3 3999879003_R02C01
startsnp=rs6838825 endsnp=rs11944122 conf=13.549
chr4:70917031-70921324 numsnp=8 length=4,294 state5,cn=3 3999879003_R02C01
startsnp=rs6853611 endsnp=variant.81303 conf=5.367
chr4:104053867-104062206 numsnp=15 length=8,340 state5,cn=3
3999879003_R02C01 startsnp=exm416552 endsnp=exm416602 conf=13.232
chr4:161875145-161927775 numsnp=4 length=52,631 state5,cn=3
3999879003_R02C01 startsnp=rs4529002 endsnp=psy_rs80120634 conf=0.872
chr4:163032521-163048238 numsnp=6 length=15,718 state5,cn=3
3999879003_R02C01 startsnp=exm432144 endsnp=rs1032394 conf=7.322
chr4:167571068-167663664 numsnp=13 length=92,597 state5,cn=3
3999879003_R02C01 startsnp=rs28713613 endsnp=rs7691894 conf=12.811
chr5:77458150-77523963 numsnp=11 length=65,814 state5,cn=3
3999879003_R02C01 startsnp=rs4704484 endsnp=variant.85363 conf=13.039
chr5:103771206-103838556 numsnp=6 length=67,351 state5,cn=3
3999879003_R02C01 startsnp=rs1442111 endsnp=rs11747766 conf=8.957
chr5:108799341-108814740 numsnp=4 length=15,400 state5,cn=3
3999879003_R02C01 startsnp=rs11241020 endsnp=rs12660042 conf=0.222
chr6:56917508-56920804 numsnp=19 length=3,297 state5,cn=3
3999879003_R02C01 startsnp=exm558038 endsnp=rs12190575 conf=12.133
chr7:85117732-85148963 numsnp=6 length=31,232 state5,cn=3
3999879003_R02C01 startsnp=rs4728584 endsnp=exm2262367 conf=4.211
chr7:93890183-93904860 numsnp=5 length=14,678 state5,cn=3
3999879003_R02C01 startsnp=rs10228755 endsnp=rs2024362 conf=4.478
chr7:102331791-102448819 numsnp=9 length=117,029 state5,cn=3
3999879003_R02C01 startsnp=kgp839309 endsnp=exm646825 conf=10.958
chr8:79334466-79347559 numsnp=3 length=13,094 state5,cn=3
3999879003_R02C01 startsnp=rs7010579 endsnp=rs7833623 conf=2.098
chr8:92479701-92534317 numsnp=5 length=54,617 state5,cn=3
3999879003_R02C01 startsnp=rs1505219 endsnp=psy_rs76579804 conf=6.464
chr8:132304508-132367143 numsnp=15 length=62,636 state5,cn=3
3999879003_R02C01 startsnp=rs10102742 endsnp=rs4570136 conf=11.773
chr9:30187798-30219494 numsnp=4 length=31,697 state5,cn=3
3999879003_R02C01 startsnp=rs7868434 endsnp=rs2769643 conf=1.415
chr9:86615956-86625243 numsnp=15 length=9,288 state5,cn=3
3999879003_R02C01 startsnp=exm758320 endsnp=rs6559758 conf=12.799
chr9:95222775-95273013 numsnp=28 length=50,239 state5,cn=3
3999879003_R02C01 startsnp=exm761527 endsnp=rs715846 conf=16.811
chr10:17312690-17352930 numsnp=9 length=40,241 state5,cn=3
3999879003_R02C01 startsnp=rs10904915 endsnp=rs452281 conf=2.906
chr10:90356072-90366587 numsnp=10 length=10,516 state5,cn=3
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chr10:91474900-91497440 numsnp=26 length=22,541 state5,cn=3
3999879003_R02C01 startsnp=exm1687268 endsnp=exm841041 conf=15.844
chr11:5905557-5908939 numsnp=18 length=3,383 state5,cn=3 3999879003_R02C01
startsnp=exm884118 endsnp=rs1453433 conf=8.906
chr11:11848522-11885841 numsnp=4 length=37,320 state5,cn=3
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chr11:99774472-99781954 numsnp=5 length=7,483 state5,cn=3
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chr12:8018538-8126839 numsnp=23 length=108,302 state5,cn=3
3999879003_R02C01 startsnp=rs11056210 endsnp=psy_rs6488802 conf=33.485
chr12:42481607-42481732 numsnp=6 length=126 state5,cn=3 3999879003_R02C01
startsnp=exm995166 endsnp=rs7972986 conf=0.437
chr12:57777755-57792580 numsnp=3 length=14,826 state5,cn=3
3999879003_R02C01 startsnp=rs34453452 endsnp=rs11613352 conf=5.798
chr12:74962715-75034433 numsnp=9 length=71,719 state5,cn=3
3999879003_R02C01 startsnp=rs10879808 endsnp=rs6582234 conf=9.119
chr12:78054695-78135318 numsnp=7 length=80,624 state5,cn=3
3999879003_R02C01 startsnp=rs1727860 endsnp=rs10859297 conf=4.555
chr13:92907738-92941096 numsnp=7 length=33,359 state5,cn=3
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chr15:97729447-97758369 numsnp=5 length=28,923 state5,cn=3
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chr16:74550997-74584311 numsnp=11 length=33,315 state5,cn=3
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chr17:29476309-29533315 numsnp=9 length=57,007 state5,cn=3
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chr18:1189998-1248578 numsnp=5 length=58,581 state5,cn=3 3999879003_R02C01
startsnp=rs11660040 endsnp=rs1939948 conf=7.781
chr18:13731520-13732454 numsnp=9 length=935 state5,cn=3 3999879003_R02C01
startsnp=exm1376929 endsnp=rs8096764 conf=1.255
chr18:36959010-36964398 numsnp=3 length=5,389 state5,cn=3
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chr19:20682055-20793615 numsnp=15 length=111,561 state5,cn=3
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chr19:21687939-21720803 numsnp=16 length=32,865 state5,cn=3
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chr19:23829737-23930879 numsnp=19 length=101,143 state5,cn=3
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chr20:15027713-15054436 numsnp=7 length=26,724 state5,cn=3
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chr20:58440438-58502456 numsnp=46 length=62,019 state5,cn=3
3999879003_R02C01 startsnp=variant.68971 endsnp=rs6100654 conf=13.246
chr10:18840868-18859719 numsnp=7 length=18,852 state6,cn=4
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chr12:133046268-133046915 numsnp=4 length=648 state6,cn=4
3999879003_R02C01 startsnp=psy_rs12228614 endsnp=psy_rs4883588 conf=4.915
chrX:4344090-4453846 numsnp=7 length=109,757 state5,cn=3 3999879003_R02C01
startsnp=rs6639996 endsnp=rs6640316 conf=2.394
chrX:9165588-9220036 numsnp=9 length=54,449 state5,cn=3 3999879003_R02C01
startsnp=rs5979044 endsnp=snv-rs146780751 conf=6.955
chrX:12208323-12282226 numsnp=13 length=73,904 state5,cn=3
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chrX:21698093-21729299 numsnp=3 length=31,207 state5,cn=3
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chrX:23522899-23571087 numsnp=5 length=48,189 state5,cn=3
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chrX:26719303-26794876 numsnp=7 length=75,574 state5,cn=3
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chrX:27104934-27677158 numsnp=32 length=572,225 state5,cn=3
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chrX:32388364-32851060 numsnp=91 length=462,697 state5,cn=3
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chrX:69772848-70094179 numsnp=31 length=321,332 state5,cn=3
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chrX:75954458-76059596 numsnp=7 length=105,139 state5,cn=3
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chrX:78555305-78703371 numsnp=18 length=148,067 state5,cn=3
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chrX:84612645-84706371 numsnp=9 length=93,727 state5,cn=3
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chrX:87376702-87457802 numsnp=11 length=81,101 state5,cn=3
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chrX:89315249-89426479 numsnp=7 length=111,231 state5,cn=3
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chrX:93457415-93530523 numsnp=9 length=73,109 state5,cn=3
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chrX:94260972-94425513 numsnp=12 length=164,542 state5,cn=3
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chrX:95257075-95508808 numsnp=22 length=251,734 state5,cn=3
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chrX:121251411-121624350 numsnp=39 length=372,940 state5,cn=3
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chrX:124669231-124885772 numsnp=14 length=216,542 state5,cn=3
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chrX:126157448-126249850 numsnp=9 length=92,403 state5,cn=3
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chrX:129335721-129442517 numsnp=11 length=106,797 state5,cn=3
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chr5:70307162-70308607 numsnp=9 length=1,446 state1,cn=0 3999879003_R09C02
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chr6:57587550-57620876 numsnp=3 length=33,327 state1,cn=0
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conf=10.341
chr8:15402936-15411023 numsnp=3 length=8,088 state1,cn=0 3999879003_R09C02
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chr1:186684977-186746556 numsnp=7 length=61,580 state5,cn=3
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chr2:13903204-13916789 numsnp=4 length=13,586 state5,cn=3
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chr2:20096767-20113967 numsnp=15 length=17,201 state5,cn=3
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chr2:45640257-45646971 numsnp=8 length=6,715 state5,cn=3 3999879003_R09C02
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chr2:90108545-90109261 numsnp=5 length=717 state5,cn=3 3999879003_R09C02
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chr2:128757970-128818557 numsnp=10 length=60,588 state5,cn=3
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chr3:144883424-144898708 numsnp=4 length=15,285 state5,cn=3
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chr3:163096848-163233510 numsnp=7 length=136,663 state5,cn=3
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chr4:63975710-64103715 numsnp=13 length=128,006 state5,cn=3
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chr5:20740586-20865083 numsnp=7 length=124,498 state5,cn=3
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chr5:77458150-77579205 numsnp=14 length=121,056 state5,cn=3
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chr6:7373356-7374207 numsnp=9 length=852 state5,cn=3 3999879003_R09C02
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chr7:80699883-80718358 numsnp=5 length=18,476 state5,cn=3
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chr7:87249057-87418861 numsnp=11 length=169,805 state5,cn=3
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chr9:30187798-30219494 numsnp=4 length=31,697 state5,cn=3
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chr10:7899231-7923508 numsnp=3 length=24,278 state5,cn=3 3999879003_R09C02
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chr10:56790969-56817533 numsnp=3 length=26,565 state5,cn=3
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chr12:77943018-77949236 numsnp=3 length=6,219 state5,cn=3
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chr13:114930955-114939396 numsnp=4 length=8,442 state5,cn=3
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chr15:24606732-24668007 numsnp=4 length=61,276 state5,cn=3
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chr17:34436708-34477887 numsnp=14 length=41,180 state5,cn=3
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chr19:54844047-54845031 numsnp=6 length=985 state5,cn=3 3999879003_R09C02
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chr22:26132612-26146429 numsnp=4 length=13,818 state5,cn=3
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chrX:84122736-84195135 numsnp=6 length=72,400 state5,cn=3
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chr3:1929666-1949594 numsnp=6 length=19,929 state2,cn=1 3999879015_R02C02
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chr3:52474473-52477866 numsnp=11 length=3,394 state2,cn=1
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chr5:139931607-139931661 numsnp=25 length=55 state2,cn=1 3999879015_R02C02
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chr10:58916759-58938552 numsnp=5 length=21,794 state2,cn=1
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chr11:10313693-10327884 numsnp=3 length=14,192 state2,cn=1
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chr15:85437286-85448906 numsnp=22 length=11,621 state2,cn=1
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chr16:605481-606913 numsnp=3 length=1,433 state2,cn=1 3999879015_R02C02
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chr21:15214708-15395187 numsnp=16 length=180,480 state2,cn=1
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chr3:191408742-191423639 numsnp=3 length=14,898 state5,cn=3
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chr8:7308356-7347711 numsnp=6 length=39,356 state5,cn=3 3999879015_R02C02
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chr8:110765282-110821596 numsnp=8 length=56,315 state5,cn=3
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chr9:39098698-39103792 numsnp=4 length=5,095 state5,cn=3 3999879015_R02C02
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chr11:97431300-97443131 numsnp=3 length=11,832 state5,cn=3
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chr12:133046268-133046915 numsnp=4 length=648 state5,cn=3
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chr16:28616665-28754684 numsnp=17 length=138,020 state5,cn=3
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chr19:8334280-8339547 numsnp=3 length=5,268 state5,cn=3 3999879015_R02C02
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chrX:146119530-146328831 numsnp=16 length=209,302 state5,cn=3
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chr2:194691051-194694686 numsnp=3 length=3,636 state1,cn=0
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chr16:70045749-70089450 numsnp=3 length=43,702 state1,cn=0
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chr2:40948151-40949168 numsnp=3 length=1,018 state2,cn=1 3999879015_R03C02
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chr7:44935-67365 numsnp=7 length=22,431 state5,cn=3 3999879015_R03C02
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chr12:133046268-133046348 numsnp=3 length=81 state5,cn=3 3999879015_R03C02
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chr14:106067618-106127330 numsnp=5 length=59,713 state5,cn=3
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chr18:75817704-75829588 numsnp=4 length=11,885 state5,cn=3
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chrX:2343284-2408593 numsnp=18 length=65,310 state2,cn=1 3999879015_R03C02
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chrX:75954458-76096727 numsnp=8 length=142,270 state5,cn=3
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chrX:146119530-146328831 numsnp=16 length=209,302 state5,cn=3
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chr4:102928866-102931282 numsnp=3 length=2,417 state1,cn=0
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chr5:49466231-49470705 numsnp=6 length=4,475 state1,cn=0 3999879053_R11C01
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chr22:50228087-50239154 numsnp=6 length=11,068 state1,cn=0
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chr5:70307162-70308607 numsnp=9 length=1,446 state2,cn=1 3999879053_R11C01
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chr5:115525539-115533407 numsnp=3 length=7,869 state2,cn=1
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chr9:11909707-12013711 numsnp=14 length=104,005 state2,cn=1
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chr11:67533195-67731956 numsnp=11 length=198,762 state2,cn=1
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chr15:20177092-20192086 numsnp=6 length=14,995 state2,cn=1
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chr10:135012384-135032385 numsnp=19 length=20,002 state5,cn=3
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chr10:135080873-135089077 numsnp=26 length=8,205 state5,cn=3
9464294016_R02C01 startsnp=exm867880 endsnp=exm868076 conf=23.907
chr11:284297-290913 numsnp=18 length=6,617 state5,cn=3 9464294016_R02C01
startsnp=exm869817 endsnp=exm869893 conf=20.667
chr12:132401542-132405765 numsnp=12 length=4,224 state5,cn=3
9464294016_R02C01 startsnp=exm1052332 endsnp=exm1052408 conf=17.013
chr15:42175564-42178519 numsnp=12 length=2,956 state5,cn=3
9464294016_R02C01 startsnp=exm1152805 endsnp=exm1152837 conf=20.900
chr16:675680-683905 numsnp=12 length=8,226 state5,cn=3 9464294016_R02C01
startsnp=exm-rs763014 endsnp=exm1197392 conf=21.648
chr16:1270317-1270935 numsnp=25 length=619 state5,cn=3 9464294016_R02C01
startsnp=chr16_1270317 endsnp=chr16_1270935 conf=37.793
chr16:2140680-2147338 numsnp=20 length=6,659 state5,cn=3 9464294016_R02C01
startsnp=exm1205480 endsnp=exm1205597 conf=19.019
chr16:88570383-88601281 numsnp=14 length=30,899 state5,cn=3
9464294016_R02C01 startsnp=rs868874 endsnp=exm1267924 conf=14.239
chr17:79094122-79096115 numsnp=14 length=1,994 state5,cn=3
9464294016_R02C01 startsnp=exm1365383 endsnp=exm1365488 conf=24.110
chr17:79425367-79429005 numsnp=21 length=3,639 state5,cn=3
9464294016_R02C01 startsnp=exm1366596 endsnp=exm1366742 conf=29.533
chr17:80048271-80049206 numsnp=10 length=936 state5,cn=3 9464294016_R02C01
startsnp=exm1369369 endsnp=exm1369401 conf=16.696
chr20:60891045-60892813 numsnp=14 length=1,769 state5,cn=3
9464294016_R02C01 startsnp=exm1555652 endsnp=exm1555702 conf=28.440
chr20:62195426-62200204 numsnp=56 length=4,779 state5,cn=3
9464294016_R02C01 startsnp=exm1972360 endsnp=exm1559809 conf=30.492
chr21:47558501-47558559 numsnp=6 length=59 state5,cn=3 9464294016_R02C01
startsnp=exm1580750 endsnp=exm1580759 conf=11.380
chr22:50942805-50943101 numsnp=8 length=297 state5,cn=3 9464294016_R02C01
startsnp=exm1623108 endsnp=exm1623134 conf=20.160
chr2:194691051-194694686 numsnp=3 length=3,636 state1,cn=0
9464294016_R03C01 startsnp=psy_rs73984715 endsnp=psy_rs12987240 conf=7.425
chr12:9703054-9723763 numsnp=4 length=20,710 state1,cn=0 9464294016_R03C01
startsnp=psy_rs10843999 endsnp=psy_rs77247953 conf=6.616
chr22:50228087-50239154 numsnp=6 length=11,068 state1,cn=0
9464294016_R03C01 startsnp=psy_rs138892 endsnp=psy_rs11704466 conf=13.827
chr4:17546381-17561139 numsnp=3 length=14,759 state2,cn=1
9464294016_R03C01 startsnp=rs6843189 endsnp=rs6828925 conf=15.792
chr5:49511425-49538829 numsnp=8 length=27,405 state2,cn=1
9464294016_R03C01 startsnp=psy_rs8188088 endsnp=psy_rs577482 conf=15.998
chr6:31219869-31221914 numsnp=4 length=2,046 state2,cn=1 9464294016_R03C01
startsnp=rs9264179 endsnp=rs9264219 conf=18.167
chr7:15063833-15100749 numsnp=12 length=36,917 state2,cn=1
9464294016_R03C01 startsnp=exm-rs10244051 endsnp=rs17348054 conf=60.253
chr10:58916759-58936553 numsnp=4 length=19,795 state2,cn=1
9464294016_R03C01 startsnp=rs6481254 endsnp=rs7081958 conf=16.032
chr19:20630360-20716939 numsnp=9 length=86,580 state2,cn=1
9464294016_R03C01 startsnp=rs10408291 endsnp=psy_rs78893254 conf=24.836
chr22:39428305-39445554 numsnp=7 length=17,250 state2,cn=1
9464294016_R03C01 startsnp=exm1609339 endsnp=rs2076101 conf=18.107
chr1:752566-846808 numsnp=6 length=94,243 state5,cn=3 9464294016_R03C01
startsnp=rs3094315 endsnp=rs4475691 conf=24.455
chr1:1222895-1226889 numsnp=25 length=3,995 state5,cn=3 9464294016_R03C01
startsnp=exm2144 endsnp=exm2270 conf=22.814
chr1:110215178-110233147 numsnp=6 length=17,970 state5,cn=3
9464294016_R03C01 startsnp=rs655315 endsnp=exm-rs1056806 conf=14.110
chr2:98235080-98238538 numsnp=3 length=3,459 state5,cn=3 9464294016_R03C01
startsnp=psy_rs2692943 endsnp=psy_rs2922532 conf=14.707
chr5:139931633-139936825 numsnp=22 length=5,193 state5,cn=3
9464294016_R03C01 startsnp=exm2088587 endsnp=exm482478 conf=23.716
chr7:44935-62643 numsnp=5 length=17,709 state5,cn=3 9464294016_R03C01
startsnp=rs7456436 endsnp=rs9642256 conf=22.146
chr7:49050763-49071509 numsnp=4 length=20,747 state5,cn=3
9464294016_R03C01 startsnp=rs4256549 endsnp=rs7804817 conf=16.726
chr8:144877618-144886308 numsnp=12 length=8,691 state5,cn=3
9464294016_R03C01 startsnp=exm728035 endsnp=exm728080 conf=19.971
chr10:26922969-26993080 numsnp=12 length=70,112 state5,cn=3
9464294016_R03C01 startsnp=psy_rs61012955 endsnp=rs11015236 conf=49.469
chr10:27044667-27258640 numsnp=35 length=213,974 state5,cn=3
9464294016_R03C01 startsnp=exm815898 endsnp=rs7069690 conf=143.083
chr10:27454316-27586972 numsnp=61 length=132,657 state5,cn=3
9464294016_R03C01 startsnp=exm816306 endsnp=rs11015657 conf=119.995
chr17:34442465-34477887 numsnp=13 length=35,423 state5,cn=3
9464294016_R03C01 startsnp=psy_rs148431271 endsnp=rs4796168 conf=26.112
chr17:80541944-80545133 numsnp=22 length=3,190 state5,cn=3
9464294016_R03C01 startsnp=exm1370410 endsnp=exm1370489 conf=25.826
chr20:62194464-62196253 numsnp=20 length=1,790 state5,cn=3
9464294016_R03C01 startsnp=exm1972354 endsnp=exm1559627 conf=27.989
chrX:34432433-34449197 numsnp=3 length=16,765 state5,cn=3
9464294016_R03C01 startsnp=rs5973188 endsnp=rs4829149 conf=3.022
chrX:35873056-35941529 numsnp=9 length=68,474 state5,cn=3
9464294016_R03C01 startsnp=rs2336401 endsnp=rs13440948 conf=12.216
chrX:36007464-36007614 numsnp=3 length=151 state5,cn=3 9464294016_R03C01
startsnp=exm1633910 endsnp=rs6629027 conf=0.905
chrX:37526542-37529705 numsnp=5 length=3,164 state5,cn=3 9464294016_R03C01
startsnp=indel.107919 endsnp=kgp22779346 conf=7.238
chr4:173426583-173429510 numsnp=3 length=2,928 state1,cn=0
9464294016_R03C02 startsnp=psy_rs7693645 endsnp=psy_rs112429191 conf=8.576
chr22:50228087-50239154 numsnp=6 length=11,068 state1,cn=0
9464294016_R03C02 startsnp=psy_rs138892 endsnp=psy_rs11704466 conf=10.744
chr1:213005012-213011812 numsnp=9 length=6,801 state2,cn=1
9464294016_R03C02 startsnp=rs6694190 endsnp=rs7524203 conf=37.457
chr12:133046268-133046915 numsnp=4 length=648 state2,cn=1
9464294016_R03C02 startsnp=psy_rs12228614 endsnp=psy_rs4883588 conf=9.474
chr14:22694672-22694963 numsnp=4 length=292 state2,cn=1 9464294016_R03C02
startsnp=variant.30917 endsnp=variant.30920 conf=16.376
chr14:44507151-44519214 numsnp=4 length=12,064 state2,cn=1
9464294016_R03C02 startsnp=rs1955970 endsnp=rs6572235 conf=20.696
chr15:20161372-20192086 numsnp=7 length=30,715 state2,cn=1
9464294016_R03C02 startsnp=rs6599770 endsnp=rs4932078 conf=25.738
chr2:98235080-98238538 numsnp=3 length=3,459 state5,cn=3 9464294016_R03C02
startsnp=psy_rs2692943 endsnp=psy_rs2922532 conf=13.779
chr4:161861640-161927775 numsnp=7 length=66,136 state5,cn=3
9464294016_R03C02 startsnp=rs7436001 endsnp=psy_rs80120634 conf=28.311
chr5:139931633-139931740 numsnp=20 length=108 state5,cn=3
9464294016_R03C02 startsnp=exm2088587 endsnp=exm482463 conf=25.968
chr11:5906073-5908939 numsnp=13 length=2,867 state5,cn=3 9464294016_R03C02
startsnp=exm884139 endsnp=rs1453433 conf=35.339
chr12:7995643-8083081 numsnp=19 length=87,439 state5,cn=3
9464294016_R03C02 startsnp=psy_rs146408584 endsnp=exm981267 conf=65.156
chr20:62190628-62191475 numsnp=10 length=848 state5,cn=3 9464294016_R03C02
startsnp=exm1559350 endsnp=psy_rs3810478 conf=25.591
chr20:62326538-62328428 numsnp=8 length=1,891 state5,cn=3
9464294016_R03C02 startsnp=exm1560323 endsnp=exm1560386 conf=19.869
chrX:134947910-134947990 numsnp=3 length=81 state1,cn=0 9464294016_R03C02
startsnp=exm1658595 endsnp=exm1658607 conf=23.878
chr1:12849870-12854507 numsnp=3 length=4,638 state1,cn=0 9464294016_R05C02
startsnp=psy_rs11583964 endsnp=exm17235 conf=11.255
chr1:12919838-12921156 numsnp=11 length=1,319 state1,cn=0
9464294016_R05C02 startsnp=exm17540 endsnp=exm17593 conf=56.916
chr1:12921272-12921311 numsnp=3 length=40 state1,cn=0 9464294016_R05C02
startsnp=exm17609 endsnp=exm17613 conf=6.054
chr4:173426583-173429510 numsnp=3 length=2,928 state1,cn=0
9464294016_R05C02 startsnp=psy_rs7693645 endsnp=psy_rs112429191 conf=13.796
chr22:50228087-50239154 numsnp=6 length=11,068 state1,cn=0
9464294016_R05C02 startsnp=psy_rs138892 endsnp=psy_rs11704466 conf=7.971
chr1:12866590-12866899 numsnp=3 length=310 state2,cn=1 9464294016_R05C02
startsnp=rs848428 endsnp=rs9308457 conf=16.444
chr1:12907683-12919111 numsnp=7 length=11,429 state2,cn=1
9464294016_R05C02 startsnp=exm17419 endsnp=exm17499 conf=11.994
chr1:12921246-12921255 numsnp=4 length=10 state2,cn=1 9464294016_R05C02
startsnp=exm17603 endsnp=exm17606 conf=10.803
chr1:213005012-213011812 numsnp=9 length=6,801 state2,cn=1
9464294016_R05C02 startsnp=rs6694190 endsnp=rs7524203 conf=37.681
chr1:242059221-242064633 numsnp=4 length=5,413 state2,cn=1
9464294016_R05C02 startsnp=rs4658535 endsnp=rs7551606 conf=7.211
chr2:243020723-243048760 numsnp=3 length=28,038 state2,cn=1
9464294016_R05C02 startsnp=rs4973686 endsnp=rs12478296 conf=13.774
chr5:46345089-46362346 numsnp=15 length=17,258 state2,cn=1
9464294016_R05C02 startsnp=psy_rs35335986 endsnp=psy_rs11949371 conf=16.252
chr11:67501626-67594702 numsnp=9 length=93,077 state2,cn=1
9464294016_R05C02 startsnp=rs10791923 endsnp=kgp4770289 conf=32.658
chr11:81509575-81516733 numsnp=4 length=7,159 state2,cn=1
9464294016_R05C02 startsnp=rs1542465 endsnp=rs11232877 conf=16.049
chr15:20161372-20192086 numsnp=7 length=30,715 state2,cn=1
9464294016_R05C02 startsnp=rs6599770 endsnp=rs4932078 conf=38.538
chr1:161492587-161512848 numsnp=6 length=20,262 state5,cn=3
9464294016_R05C02 startsnp=rs12129787 endsnp=exm118068 conf=17.425
chr2:98235080-98238538 numsnp=3 length=3,459 state5,cn=3 9464294016_R05C02
startsnp=psy_rs2692943 endsnp=psy_rs2922532 conf=12.595
chr4:145009802-145038131 numsnp=8 length=28,330 state5,cn=3
9464294016_R05C02 startsnp=rs7657795 endsnp=variant.82937 conf=28.468
chr9:135951231-135962478 numsnp=3 length=11,248 state5,cn=3
9464294016_R05C02 startsnp=rs2283134 endsnp=psy_rs62576805 conf=10.887
chr10:11805412-11805494 numsnp=4 length=83 state5,cn=3 9464294016_R05C02
startsnp=exm809375 endsnp=exm809385 conf=11.177
chr17:34442465-34477887 numsnp=13 length=35,423 state5,cn=3
9464294016_R05C02 startsnp=psy_rs148431271 endsnp=rs4796168 conf=18.362
chr21:47558501-47558559 numsnp=6 length=59 state5,cn=3 9464294016_R05C02
startsnp=exm1580750 endsnp=exm1580759 conf=15.282
chrX:1216188-1558028 numsnp=61 length=341,841 state2,cn=1
9464294016_R05C02 startsnp=kgp30790682 endsnp=exm1625277 conf=13.396
chrX:2139168-2233693 numsnp=8 length=94,526 state2,cn=1 9464294016_R05C02
startsnp=exm1625569 endsnp=kgp22770430 conf=10.507
chrX:23552489-23571087 numsnp=4 length=18,599 state5,cn=3
9464294016_R05C02 startsnp=rs5925823 endsnp=rs6629682 conf=7.334
chrX:34432433-34449197 numsnp=3 length=16,765 state5,cn=3
9464294016_R05C02 startsnp=rs5973188 endsnp=rs4829149 conf=2.757
chrX:42476601-42522632 numsnp=4 length=46,032 state5,cn=3
9464294016_R05C02 startsnp=rs4827306 endsnp=snv-rs112794456 conf=4.375
chrX:149005063-149013963 numsnp=8 length=8,901 state5,cn=3
9464294016_R05C02 startsnp=rs2166782 endsnp=exm1661492 conf=3.655
chrX:153037394-153041544 numsnp=13 length=4,151 state5,cn=3
9464294016_R05C02 startsnp=exm1664088 endsnp=rs5987155 conf=9.654
chr2:194691051-194694686 numsnp=3 length=3,636 state1,cn=0
9464294016_R07C02 startsnp=psy_rs73984715 endsnp=psy_rs12987240 conf=9.060
chr4:173426583-173429510 numsnp=3 length=2,928 state1,cn=0
9464294016_R07C02 startsnp=psy_rs7693645 endsnp=psy_rs112429191 conf=8.197
chr8:39284717-39321992 numsnp=4 length=37,276 state1,cn=0
9464294016_R07C02 startsnp=psy_rs7827037 endsnp=psy_rs28851014 conf=21.822
chr2:225244304-225244923 numsnp=5 length=620 state2,cn=1 9464294016_R07C02
startsnp=variant.65840 endsnp=rs3738953 conf=19.671
chr5:139931607-139931656 numsnp=21 length=50 state2,cn=1 9464294016_R07C02
startsnp=exm482409 endsnp=exm482450 conf=36.081
chr8:24207409-24207472 numsnp=5 length=64 state2,cn=1 9464294016_R07C02
startsnp=exm690047 endsnp=exm690053 conf=19.841
chr9:11976830-11996831 numsnp=3 length=20,002 state2,cn=1
9464294016_R07C02 startsnp=rs16928298 endsnp=rs4512479 conf=12.814
chr16:72089740-72108264 numsnp=13 length=18,525 state2,cn=1
9464294016_R07C02 startsnp=rs2070937 endsnp=exm1256782 conf=14.001
chr19:20596024-20716939 numsnp=11 length=120,916 state2,cn=1
9464294016_R07C02 startsnp=psy_rs6511102 endsnp=psy_rs78893254 conf=26.229
chr1:1222596-1249194 numsnp=64 length=26,599 state5,cn=3 9464294016_R07C02
startsnp=exm2135 endsnp=indel.166 conf=30.720
chr1:3389703-3416502 numsnp=38 length=26,800 state5,cn=3 9464294016_R07C02
startsnp=exm6750 endsnp=psy_rs41307852 conf=29.808
chr2:98235080-98242427 numsnp=4 length=7,348 state5,cn=3 9464294016_R07C02
startsnp=psy_rs2692943 endsnp=kgp1336864 conf=14.091
chr2:239038829-239040270 numsnp=16 length
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Hi Kai,
I am trying to use the same PennCNV version with a previously published paper in order to make the cnv results more comparable? The PennCNV used in that paper is PennCNV v2010May01. I am not sure which version is this? Is this PennCNV v1.0.0?
Happy new year!
Best regards,
Qidi Feng
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