The three tables below summarize the rules required to transform Y chromosome positions from the hg19 build to the hg38 build. The information for these tables comes from the hg19 to hg38 chain file for the UCSC liftOver utility. The tables below are a summary of that information in a more human readable format.

This information can only be used to translate from hg19 to hg38 coordinates. The reverse process from hg38 to hg19 requires a different set of rules. Although most positions will translate in a 1-1 manner, not all will.

Although most Y chromosome positions from hg19 will map to Y chromosome positions in hg38, there are some Y chromosome positions that will map to the X chromosome, and there are also some positions that were not on the Y chromosome in hg19 that now map to the Y chromosome in hg38.

The coordinates are 1-based and both the Start and End coordinates are included in the range. This is the format that we would normally expect. It differs from the usual format for BED files used by the liftOver utility.

If anyone finds any mistakes, please let me know. Thanks.


chrY to chrY

hg19 Y positions that still map to the Y chromosome in hg38.

hg19hg19 Starthg19 Endhg38hg38 Starthg38 EndChange
chrY1000144821chrY1000144821No Change
chrY94829181384chrY228162314717Add 133333
chrY231385997520chrY3206501086785Add 89265
chrY10475751048624chrY10744761075525Add 26901
chrY10486731049362chrY10755741076263Add 26901
chrY10493811049778chrY10762811076678Add 26900
chrY10497791051230chrY10766801078131Add 26901
chrY10512431051368chrY10781321078257Add 26889
chrY10513701052576chrY10782581079464Add 26888
chrY10525871052682chrY10794751079570Add 26888
chrY10527221052963chrY10796101079851Add 26888
chrY10529671053459chrY10798521080344Add 26885
chrY10575841057699chrY10850011085116Add 27417
chrY10577001058289chrY10851181085707Add 27418
chrY10583071058386chrY10857251085804Add 27418
chrY10585341058694chrY10858051085965Add 27271
chrY10589901059358chrY10859661086334Add 26976
chrY10594411059766chrY10864171086742Add 26976
chrY10598731060043chrY10859641086134Add 26091
chrY10601701060243chrY10862611086334Add 26091
chrY10603211060435chrY10864121086526Add 26091
chrY10604361060464chrY10859371085965Add 25501
chrY10604651062058chrY10865561088149Add 26091
chrY10621491062271chrY10882391088361Add 26090
chrY10625861062719chrY10883621088495Add 25776
chrY10627211064947chrY10884961090722Add 25775
chrY10649831065421chrY10907581091196Add 25775
chrY10654341065581chrY10912091091356Add 25775
chrY10656271065669chrY10914021091444Add 25775
chrY10656701065991chrY10914491091770Add 25779
chrY10660161066190chrY10917951091969Add 25779
chrY10661991066642chrY10919781092421Add 25779
chrY10666431066997chrY10925571092911Add 25914
chrY10671701067306chrY10929491093085Add 25779
chrY10673071067671chrY10930891093453Add 25782
chrY10676951068236chrY10934771094018Add 25782
chrY10682371068761chrY10940201094544Add 25783
chrY10687641070509chrY10945451096290Add 25781
chrY10705391072298chrY10963201098079Add 25781
chrY10723011075894chrY10980801101673Add 25779
chrY10758951077750chrY11017941103649Add 25899
chrY10777581078453chrY11036571104352Add 25899
chrY10784941078917chrY11043931104816Add 25899
chrY10789181080097chrY11048211106000Add 25903
chrY10801551080274chrY11060611106180Add 25906
chrY10805301080594chrY11066151106679Add 26085
chrY10806201080688chrY11067051106773Add 26085
chrY10806891080826chrY11067781106915Add 26089
chrY10808551081799chrY11069481107892Add 26093
chrY10818301083380chrY11079231109473Add 26093
chrY10833811084113chrY11094781110210Add 26097
chrY11362201136246chrY10860671086093Subtract 50153
chrY11365701136782chrY10861221086334Subtract 50448
chrY11369391214234chrY10867861164081Subtract 50153
chrY12651151265224chrY11970011197110Subtract 68114
chrY12652321266329chrY11971151198212Subtract 68117
chrY12665371266562chrY11984121198437Subtract 68125
chrY12667901267005chrY11981811198396Subtract 68609
chrY12670381267189chrY11982131198364Subtract 68825
chrY12672221267591chrY11983651198734Subtract 68857
chrY12675981268791chrY11987351199928Subtract 68863
chrY12688141268956chrY11999351200077Subtract 68879
chrY12689591268995chrY12000781200114Subtract 68881
chrY12689981269009chrY12001151200126Subtract 68883
chrY12690111269201chrY12001281200318Subtract 68883
chrY12692051269288chrY12003241200407Subtract 68881
chrY12692901269312chrY12004081200430Subtract 68882
chrY12693151269418chrY12004311200534Subtract 68884
chrY12694191269477chrY12006421200700Subtract 68777
chrY12694791269518chrY12007021200741Subtract 68777
chrY12695201269577chrY12007431200800Subtract 68777
chrY12696291269670chrY12008011200842Subtract 68828
chrY12696711269832chrY12008451201006Subtract 68826
chrY12698341269921chrY12010081201095Subtract 68826
chrY12699231270042chrY12010971201216Subtract 68826
chrY12700441270067chrY12012181201241Subtract 68826
chrY12700691270103chrY12012431201277Subtract 68826
chrY12701141270177chrY12012781201341Subtract 68836
chrY12701821270223chrY12013421201383Subtract 68840
chrY12702251270324chrY12013851201484Subtract 68840
chrY12703251270364chrY12014891201528Subtract 68836
chrY12703991270522chrY12015291201652Subtract 68870
chrY12705271270672chrY12016531201798Subtract 68874
chrY12706731271517chrY12018031202647Subtract 68870
chrY12715181271964chrY12026491203095Subtract 68869
chrY12719651272939chrY12030991204073Subtract 68866
chrY12729741273028chrY12040971204151Subtract 68877
chrY12730452018238chrY12041521949345Subtract 68893
chrY20682392069270chrY22002652201296Add 132026
chrY20692732069395chrY22012972201419Add 132024
chrY20693972069417chrY22014212201441Add 132024
chrY20694192069955chrY22014432201979Add 132024
chrY20699882070010chrY22019802202002Add 131992
chrY20700112070555chrY22020112202555Add 132000
chrY20705582070581chrY22025582202581Add 132000
chrY20705842071038chrY22025822203036Add 131998
chrY20710462071295chrY22030412203290Add 131995
chrY20712972071327chrY22032922203322Add 131995
chrY20713292071676chrY22033242203671Add 131995
chrY20716782071726chrY22036732203721Add 131995
chrY20717282072326chrY22037232204321Add 131995
chrY20723282072349chrY22043232204344Add 131995
chrY20723512073072chrY22043462205067Add 131995
chrY20730742073093chrY22050692205088Add 131995
chrY20730942073165chrY22050902205161Add 131996
chrY20731672073252chrY22051632205248Add 131996
chrY20732612073511chrY22052572205507Add 131996
chrY20735132073570chrY22055092205566Add 131996
chrY20735722073721chrY22055682205717Add 131996
chrY20737232073764chrY22057192205760Add 131996
chrY20737662073826chrY22057622205822Add 131996
chrY20738302073908chrY22058232205901Add 131993
chrY20739102074063chrY22059032206056Add 131993
chrY20740652074092chrY22060582206085Add 131993
chrY20740942074612chrY22060872206605Add 131993
chrY20746992075257chrY22066862207244Add 131987
chrY20752592075308chrY22072482207297Add 131989
chrY20753112075319chrY22072982207306Add 131987
chrY20753302075596chrY22073072207573Add 131977
chrY20755982075615chrY22075742207591Add 131976
chrY20756172076218chrY22075932208194Add 131976
chrY20762202076571chrY22081952208546Add 131975
chrY20765722076980chrY22085482208956Add 131976
chrY20769902077179chrY22089662209155Add 131976
chrY20771872077245chrY22091652209223Add 131978
chrY20772532077379chrY22092332209359Add 131980
chrY20773802078020chrY22093612210001Add 131981
chrY20780222078890chrY22100022210870Add 131980
chrY20788932079272chrY22108712211250Add 131978
chrY20792852079322chrY22112512211288Add 131966
chrY20793312079357chrY22112892211315Add 131958
chrY20793592080049chrY22113172212007Add 131958
chrY20800502080174chrY22120092212133Add 131959
chrY20801768914955chrY22121359046914Add 131959
chrY89649569241322chrY91273479403713Add 162391
chrY929132310104553chrY945371410266944Add 162391
chrY1310455413143954chrY1059404010633440Subtract 2510514
chrY1319395513748578chrY1103827911592902Subtract 2155676
chrY1379857914334339chrY1167787312213633Subtract 2120706
chrY1433434014367258chrY1221363512246553Subtract 2120705
chrY1436727014398979chrY1224656612278275Subtract 2120704
chrY1439898114399101chrY1227827712278397Subtract 2120704
chrY1439910614406362chrY1227840312285659Subtract 2120703
chrY1440636314409003chrY1228566112288301Subtract 2120702
chrY1440900514418151chrY1228830212297448Subtract 2120703
chrY1441817414429405chrY1229744912308680Subtract 2120725
chrY1442940814435781chrY1230868112315054Subtract 2120727
chrY1443578314435817chrY1231505612315090Subtract 2120727
chrY1443581914466994chrY1231509212346267Subtract 2120727
chrY1446699914491215chrY1234626812370484Subtract 2120731
chrY1449132214496297chrY1237951912384494Subtract 2111803
chrY1449629814515312chrY1238450312403517Subtract 2111795
chrY1451531714562321chrY1240351812450522Subtract 2111799
chrY1456232314600822chrY1245052312489022Subtract 2111800
chrY1460082314610880chrY1248902512499082Subtract 2111798
chrY1461088114612456chrY1249908712500662Subtract 2111794
chrY1461246514624253chrY1250066312512451Subtract 2111802
chrY1462429514625233chrY1251249512513433Subtract 2111800
chrY1462523414625776chrY1251350212514044Subtract 2111732
chrY1462577814625844chrY1251404612514112Subtract 2111732
chrY1462584814625901chrY1251411712514170Subtract 2111731
chrY1462610314626143chrY1251417112514211Subtract 2111932
chrY1462615014626189chrY1251421812514257Subtract 2111932
chrY1462619114629583chrY1251425912517651Subtract 2111932
chrY1462958414630333chrY1251765312518402Subtract 2111931
chrY1463033514630356chrY1251840412518425Subtract 2111931
chrY1463035814644697chrY1251842712532766Subtract 2111931
chrY1464469914644741chrY1253276812532810Subtract 2111931
chrY1464474314645390chrY1253281212533459Subtract 2111931
chrY1464539614646837chrY1253346012534901Subtract 2111936
chrY1464683814664253chrY1253490312552318Subtract 2111935
chrY1466425414667681chrY1255232012555747Subtract 2111934
chrY1466768314667817chrY1255574812555882Subtract 2111935
chrY1466781814709275chrY1255588412597341Subtract 2111934
chrY1470928114716431chrY1259734812604498Subtract 2111933
chrY1471643214743413chrY1260450012631481Subtract 2111932
chrY1474341414778454chrY1263148312666523Subtract 2111931
chrY1477845514787828chrY1266652512675898Subtract 2111930
chrY1478782914819043chrY1267590012707114Subtract 2111929
chrY1481904814842406chrY1270711512730473Subtract 2111933
chrY1484240814866140chrY1273047412754206Subtract 2111934
chrY1486614114881707chrY1275421112769777Subtract 2111930
chrY1488171014882304chrY1276977812770372Subtract 2111932
chrY1488230714898435chrY1277037312786501Subtract 2111934
chrY1489843614919271chrY1278650312807338Subtract 2111933
chrY1491927414937823chrY1280733912825888Subtract 2111935
chrY1493782414938630chrY1282589912826705Subtract 2111925
chrY1493863214954404chrY1282670612842478Subtract 2111926
chrY1495440514977709chrY1284248012865784Subtract 2111925
chrY1497771014981833chrY1286578612869909Subtract 2111924
chrY1498184214986718chrY1286991012874786Subtract 2111932
chrY1498672114989218chrY1287478712877284Subtract 2111934
chrY1498921915011301chrY1287730412899386Subtract 2111915
chrY1501130215015255chrY1289939012903343Subtract 2111912
chrY1501525615022824chrY1290334512910913Subtract 2111911
chrY1502282615037754chrY1291091412925842Subtract 2111912
chrY1503775515047299chrY1292584512935389Subtract 2111910
chrY1504730015055137chrY1293539112943228Subtract 2111909
chrY1505513815066205chrY1294323012954297Subtract 2111908
chrY1506620715072595chrY1295429812960686Subtract 2111909
chrY1507259715088608chrY1296068712976698Subtract 2111910
chrY1508861015092756chrY1297669912980845Subtract 2111911
chrY1509275815106783chrY1298084612994871Subtract 2111912
chrY1510678515157860chrY1299487213045947Subtract 2111913
chrY1515786215255769chrY1304594813143855Subtract 2111914
chrY1525577215263356chrY1314385613151440Subtract 2111916
chrY1526335715264729chrY1315144713152819Subtract 2111910
chrY1526473115278820chrY1315282013166909Subtract 2111911
chrY1527882215305843chrY1316692113193942Subtract 2111901
chrY1530584415308826chrY1319394613196928Subtract 2111898
chrY1530882715309739chrY1319693113197843Subtract 2111896
chrY1530974015315461chrY1319784513203566Subtract 2111895
chrY1531546215320664chrY1320356813208770Subtract 2111894
chrY1532066515340383chrY1320878313228501Subtract 2111882
chrY1534038415358761chrY1322850313246880Subtract 2111881
chrY1535876220143882chrY1324688218032002Subtract 2111880
chrY2019388922369679chrY1803200320207793Subtract 2161886
chrY2241968023901428chrY2025779421739542Subtract 2161886
chrY2395142928819361chrY2180528226673214Subtract 2146147
chrY5881936258917656chrY5677150956673215Shift and Reverse Conjugate
chrY5896765759052824chrY5682151056906677Subtract 2146147
chrY5905282659131404chrY5690667856985256Subtract 2146148
chrY5913140659194901chrY5698525757048752Subtract 2146149
chrY5919490359198059chrY5704875357051909Subtract 2146150
chrY5919806059228441chrY5705191157082292Subtract 2146149
chrY5922844359282590chrY5708229357136440Subtract 2146150
chrY5928259259363566chrY5713644157217415Subtract 2146151

chrY to chrX

hg19 Y positions that now map to the X chromosome in hg38.

hg19hg19 Starthg19 Endhg38hg38 Starthg38 EndChange
chrY10534771056575chrX10803621083460Add 26885
chrY10565951056773chrX10834781083656Add 26883
chrY10568221056893chrX10837051083776Add 26883
chrY10569421056994chrX10838261083878Add 26884
chrY10569951057054chrX10839381083997Add 26943
chrY10570611057080chrX10840041084023Add 26943
chrY10570811057583chrX10844981085000Add 27417
chrY10586951058989chrX10862611086555Add 27566
chrY10593591059440chrX10860401086121Add 26681
chrY10597671059872chrX10861531086258Add 26386
chrY10600441060169chrX10864301086555Add 26386
chrY11341141134395chrX10848451085126Subtract 49269
chrY11343991135088chrX10851311085820Subtract 49268
chrY11350981135360chrX10858301086092Subtract 49268
chrY11353611135402chrX10863881086429Subtract 48973
chrY11354041135444chrX10858411085881Subtract 49563
chrY11354451135924chrX10861771086656Subtract 49268
chrY11359251136192chrX10860671086334Subtract 49858
chrY11361931136219chrX10866301086656Subtract 49563
chrY11362471136487chrX10863891086629Subtract 49858
chrY11367831136809chrX10860401086066Subtract 50743
chrY12663371266396chrX11981561198215Subtract 68181
chrY12664011266536chrX11982161198351Subtract 68185
chrY12665631266609chrX11983781198424Subtract 68185
chrY12666101266641chrX11982411198272Subtract 68369
chrY12666421266669chrX11982131198240Subtract 68429
chrY12666701266734chrX11984251198489Subtract 68245
chrY12667351266761chrX11982461198272Subtract 68489

chrX to chrY

hg19 X positions that now map to the Y chromosome in hg38.

hg19hg19 Starthg19 Endhg38hg38 Starthg38 EndChange
chrX11086951108989chrY10862611086555Subtract 22434
chrX11853611185402chrY10863881086429Subtract 98973
chrX11854041185444chrY10858411085881Subtract 99563
chrX11859251186192chrY10860671086334Subtract 99858
chrX11862201186246chrY10860671086093Subtract 100153
chrX11862471186487chrY10863891086629Subtract 99858
chrX11865701186782chrY10861221086334Subtract 100448
chrX11867831186809chrY10860401086066Subtract 100743
chrX13163371316396chrY11981561198215Subtract 118181
chrX13164011316536chrY11982161198351Subtract 118185
chrX13165631316609chrY11983781198424Subtract 118185
chrX13166701316734chrY11984251198489Subtract 118245
chrX13167901317005chrY11981811198396Subtract 118609
chrX115148083115148144chrY1495667814956617Shift and Reverse Conjugate