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.

hg19	hg19 Start	hg19 End	hg38	hg38 Start	hg38 End	Change
chrY	10001	44821	chrY	10001	44821	No Change
chrY	94829	181384	chrY	228162	314717	Add 133333
chrY	231385	997520	chrY	320650	1086785	Add 89265
chrY	1047575	1048624	chrY	1074476	1075525	Add 26901
chrY	1048673	1049362	chrY	1075574	1076263	Add 26901
chrY	1049381	1049778	chrY	1076281	1076678	Add 26900
chrY	1049779	1051230	chrY	1076680	1078131	Add 26901
chrY	1051243	1051368	chrY	1078132	1078257	Add 26889
chrY	1051370	1052576	chrY	1078258	1079464	Add 26888
chrY	1052587	1052682	chrY	1079475	1079570	Add 26888
chrY	1052722	1052963	chrY	1079610	1079851	Add 26888
chrY	1052967	1053459	chrY	1079852	1080344	Add 26885
chrY	1057584	1057699	chrY	1085001	1085116	Add 27417
chrY	1057700	1058289	chrY	1085118	1085707	Add 27418
chrY	1058307	1058386	chrY	1085725	1085804	Add 27418
chrY	1058534	1058694	chrY	1085805	1085965	Add 27271
chrY	1058990	1059358	chrY	1085966	1086334	Add 26976
chrY	1059441	1059766	chrY	1086417	1086742	Add 26976
chrY	1059873	1060043	chrY	1085964	1086134	Add 26091
chrY	1060170	1060243	chrY	1086261	1086334	Add 26091
chrY	1060321	1060435	chrY	1086412	1086526	Add 26091
chrY	1060436	1060464	chrY	1085937	1085965	Add 25501
chrY	1060465	1062058	chrY	1086556	1088149	Add 26091
chrY	1062149	1062271	chrY	1088239	1088361	Add 26090
chrY	1062586	1062719	chrY	1088362	1088495	Add 25776
chrY	1062721	1064947	chrY	1088496	1090722	Add 25775
chrY	1064983	1065421	chrY	1090758	1091196	Add 25775
chrY	1065434	1065581	chrY	1091209	1091356	Add 25775
chrY	1065627	1065669	chrY	1091402	1091444	Add 25775
chrY	1065670	1065991	chrY	1091449	1091770	Add 25779
chrY	1066016	1066190	chrY	1091795	1091969	Add 25779
chrY	1066199	1066642	chrY	1091978	1092421	Add 25779
chrY	1066643	1066997	chrY	1092557	1092911	Add 25914
chrY	1067170	1067306	chrY	1092949	1093085	Add 25779
chrY	1067307	1067671	chrY	1093089	1093453	Add 25782
chrY	1067695	1068236	chrY	1093477	1094018	Add 25782
chrY	1068237	1068761	chrY	1094020	1094544	Add 25783
chrY	1068764	1070509	chrY	1094545	1096290	Add 25781
chrY	1070539	1072298	chrY	1096320	1098079	Add 25781
chrY	1072301	1075894	chrY	1098080	1101673	Add 25779
chrY	1075895	1077750	chrY	1101794	1103649	Add 25899
chrY	1077758	1078453	chrY	1103657	1104352	Add 25899
chrY	1078494	1078917	chrY	1104393	1104816	Add 25899
chrY	1078918	1080097	chrY	1104821	1106000	Add 25903
chrY	1080155	1080274	chrY	1106061	1106180	Add 25906
chrY	1080530	1080594	chrY	1106615	1106679	Add 26085
chrY	1080620	1080688	chrY	1106705	1106773	Add 26085
chrY	1080689	1080826	chrY	1106778	1106915	Add 26089
chrY	1080855	1081799	chrY	1106948	1107892	Add 26093
chrY	1081830	1083380	chrY	1107923	1109473	Add 26093
chrY	1083381	1084113	chrY	1109478	1110210	Add 26097
chrY	1136220	1136246	chrY	1086067	1086093	Subtract 50153
chrY	1136570	1136782	chrY	1086122	1086334	Subtract 50448
chrY	1136939	1214234	chrY	1086786	1164081	Subtract 50153
chrY	1265115	1265224	chrY	1197001	1197110	Subtract 68114
chrY	1265232	1266329	chrY	1197115	1198212	Subtract 68117
chrY	1266537	1266562	chrY	1198412	1198437	Subtract 68125
chrY	1266790	1267005	chrY	1198181	1198396	Subtract 68609
chrY	1267038	1267189	chrY	1198213	1198364	Subtract 68825
chrY	1267222	1267591	chrY	1198365	1198734	Subtract 68857
chrY	1267598	1268791	chrY	1198735	1199928	Subtract 68863
chrY	1268814	1268956	chrY	1199935	1200077	Subtract 68879
chrY	1268959	1268995	chrY	1200078	1200114	Subtract 68881
chrY	1268998	1269009	chrY	1200115	1200126	Subtract 68883
chrY	1269011	1269201	chrY	1200128	1200318	Subtract 68883
chrY	1269205	1269288	chrY	1200324	1200407	Subtract 68881
chrY	1269290	1269312	chrY	1200408	1200430	Subtract 68882
chrY	1269315	1269418	chrY	1200431	1200534	Subtract 68884
chrY	1269419	1269477	chrY	1200642	1200700	Subtract 68777
chrY	1269479	1269518	chrY	1200702	1200741	Subtract 68777
chrY	1269520	1269577	chrY	1200743	1200800	Subtract 68777
chrY	1269629	1269670	chrY	1200801	1200842	Subtract 68828
chrY	1269671	1269832	chrY	1200845	1201006	Subtract 68826
chrY	1269834	1269921	chrY	1201008	1201095	Subtract 68826
chrY	1269923	1270042	chrY	1201097	1201216	Subtract 68826
chrY	1270044	1270067	chrY	1201218	1201241	Subtract 68826
chrY	1270069	1270103	chrY	1201243	1201277	Subtract 68826
chrY	1270114	1270177	chrY	1201278	1201341	Subtract 68836
chrY	1270182	1270223	chrY	1201342	1201383	Subtract 68840
chrY	1270225	1270324	chrY	1201385	1201484	Subtract 68840
chrY	1270325	1270364	chrY	1201489	1201528	Subtract 68836
chrY	1270399	1270522	chrY	1201529	1201652	Subtract 68870
chrY	1270527	1270672	chrY	1201653	1201798	Subtract 68874
chrY	1270673	1271517	chrY	1201803	1202647	Subtract 68870
chrY	1271518	1271964	chrY	1202649	1203095	Subtract 68869
chrY	1271965	1272939	chrY	1203099	1204073	Subtract 68866
chrY	1272974	1273028	chrY	1204097	1204151	Subtract 68877
chrY	1273045	2018238	chrY	1204152	1949345	Subtract 68893
chrY	2068239	2069270	chrY	2200265	2201296	Add 132026
chrY	2069273	2069395	chrY	2201297	2201419	Add 132024
chrY	2069397	2069417	chrY	2201421	2201441	Add 132024
chrY	2069419	2069955	chrY	2201443	2201979	Add 132024
chrY	2069988	2070010	chrY	2201980	2202002	Add 131992
chrY	2070011	2070555	chrY	2202011	2202555	Add 132000
chrY	2070558	2070581	chrY	2202558	2202581	Add 132000
chrY	2070584	2071038	chrY	2202582	2203036	Add 131998
chrY	2071046	2071295	chrY	2203041	2203290	Add 131995
chrY	2071297	2071327	chrY	2203292	2203322	Add 131995
chrY	2071329	2071676	chrY	2203324	2203671	Add 131995
chrY	2071678	2071726	chrY	2203673	2203721	Add 131995
chrY	2071728	2072326	chrY	2203723	2204321	Add 131995
chrY	2072328	2072349	chrY	2204323	2204344	Add 131995
chrY	2072351	2073072	chrY	2204346	2205067	Add 131995
chrY	2073074	2073093	chrY	2205069	2205088	Add 131995
chrY	2073094	2073165	chrY	2205090	2205161	Add 131996
chrY	2073167	2073252	chrY	2205163	2205248	Add 131996
chrY	2073261	2073511	chrY	2205257	2205507	Add 131996
chrY	2073513	2073570	chrY	2205509	2205566	Add 131996
chrY	2073572	2073721	chrY	2205568	2205717	Add 131996
chrY	2073723	2073764	chrY	2205719	2205760	Add 131996
chrY	2073766	2073826	chrY	2205762	2205822	Add 131996
chrY	2073830	2073908	chrY	2205823	2205901	Add 131993
chrY	2073910	2074063	chrY	2205903	2206056	Add 131993
chrY	2074065	2074092	chrY	2206058	2206085	Add 131993
chrY	2074094	2074612	chrY	2206087	2206605	Add 131993
chrY	2074699	2075257	chrY	2206686	2207244	Add 131987
chrY	2075259	2075308	chrY	2207248	2207297	Add 131989
chrY	2075311	2075319	chrY	2207298	2207306	Add 131987
chrY	2075330	2075596	chrY	2207307	2207573	Add 131977
chrY	2075598	2075615	chrY	2207574	2207591	Add 131976
chrY	2075617	2076218	chrY	2207593	2208194	Add 131976
chrY	2076220	2076571	chrY	2208195	2208546	Add 131975
chrY	2076572	2076980	chrY	2208548	2208956	Add 131976
chrY	2076990	2077179	chrY	2208966	2209155	Add 131976
chrY	2077187	2077245	chrY	2209165	2209223	Add 131978
chrY	2077253	2077379	chrY	2209233	2209359	Add 131980
chrY	2077380	2078020	chrY	2209361	2210001	Add 131981
chrY	2078022	2078890	chrY	2210002	2210870	Add 131980
chrY	2078893	2079272	chrY	2210871	2211250	Add 131978
chrY	2079285	2079322	chrY	2211251	2211288	Add 131966
chrY	2079331	2079357	chrY	2211289	2211315	Add 131958
chrY	2079359	2080049	chrY	2211317	2212007	Add 131958
chrY	2080050	2080174	chrY	2212009	2212133	Add 131959
chrY	2080176	8914955	chrY	2212135	9046914	Add 131959
chrY	8964956	9241322	chrY	9127347	9403713	Add 162391
chrY	9291323	10104553	chrY	9453714	10266944	Add 162391
chrY	13104554	13143954	chrY	10594040	10633440	Subtract 2510514
chrY	13193955	13748578	chrY	11038279	11592902	Subtract 2155676
chrY	13798579	14334339	chrY	11677873	12213633	Subtract 2120706
chrY	14334340	14367258	chrY	12213635	12246553	Subtract 2120705
chrY	14367270	14398979	chrY	12246566	12278275	Subtract 2120704
chrY	14398981	14399101	chrY	12278277	12278397	Subtract 2120704
chrY	14399106	14406362	chrY	12278403	12285659	Subtract 2120703
chrY	14406363	14409003	chrY	12285661	12288301	Subtract 2120702
chrY	14409005	14418151	chrY	12288302	12297448	Subtract 2120703
chrY	14418174	14429405	chrY	12297449	12308680	Subtract 2120725
chrY	14429408	14435781	chrY	12308681	12315054	Subtract 2120727
chrY	14435783	14435817	chrY	12315056	12315090	Subtract 2120727
chrY	14435819	14466994	chrY	12315092	12346267	Subtract 2120727
chrY	14466999	14491215	chrY	12346268	12370484	Subtract 2120731
chrY	14491322	14496297	chrY	12379519	12384494	Subtract 2111803
chrY	14496298	14515312	chrY	12384503	12403517	Subtract 2111795
chrY	14515317	14562321	chrY	12403518	12450522	Subtract 2111799
chrY	14562323	14600822	chrY	12450523	12489022	Subtract 2111800
chrY	14600823	14610880	chrY	12489025	12499082	Subtract 2111798
chrY	14610881	14612456	chrY	12499087	12500662	Subtract 2111794
chrY	14612465	14624253	chrY	12500663	12512451	Subtract 2111802
chrY	14624295	14625233	chrY	12512495	12513433	Subtract 2111800
chrY	14625234	14625776	chrY	12513502	12514044	Subtract 2111732
chrY	14625778	14625844	chrY	12514046	12514112	Subtract 2111732
chrY	14625848	14625901	chrY	12514117	12514170	Subtract 2111731
chrY	14626103	14626143	chrY	12514171	12514211	Subtract 2111932
chrY	14626150	14626189	chrY	12514218	12514257	Subtract 2111932
chrY	14626191	14629583	chrY	12514259	12517651	Subtract 2111932
chrY	14629584	14630333	chrY	12517653	12518402	Subtract 2111931
chrY	14630335	14630356	chrY	12518404	12518425	Subtract 2111931
chrY	14630358	14644697	chrY	12518427	12532766	Subtract 2111931
chrY	14644699	14644741	chrY	12532768	12532810	Subtract 2111931
chrY	14644743	14645390	chrY	12532812	12533459	Subtract 2111931
chrY	14645396	14646837	chrY	12533460	12534901	Subtract 2111936
chrY	14646838	14664253	chrY	12534903	12552318	Subtract 2111935
chrY	14664254	14667681	chrY	12552320	12555747	Subtract 2111934
chrY	14667683	14667817	chrY	12555748	12555882	Subtract 2111935
chrY	14667818	14709275	chrY	12555884	12597341	Subtract 2111934
chrY	14709281	14716431	chrY	12597348	12604498	Subtract 2111933
chrY	14716432	14743413	chrY	12604500	12631481	Subtract 2111932
chrY	14743414	14778454	chrY	12631483	12666523	Subtract 2111931
chrY	14778455	14787828	chrY	12666525	12675898	Subtract 2111930
chrY	14787829	14819043	chrY	12675900	12707114	Subtract 2111929
chrY	14819048	14842406	chrY	12707115	12730473	Subtract 2111933
chrY	14842408	14866140	chrY	12730474	12754206	Subtract 2111934
chrY	14866141	14881707	chrY	12754211	12769777	Subtract 2111930
chrY	14881710	14882304	chrY	12769778	12770372	Subtract 2111932
chrY	14882307	14898435	chrY	12770373	12786501	Subtract 2111934
chrY	14898436	14919271	chrY	12786503	12807338	Subtract 2111933
chrY	14919274	14937823	chrY	12807339	12825888	Subtract 2111935
chrY	14937824	14938630	chrY	12825899	12826705	Subtract 2111925
chrY	14938632	14954404	chrY	12826706	12842478	Subtract 2111926
chrY	14954405	14977709	chrY	12842480	12865784	Subtract 2111925
chrY	14977710	14981833	chrY	12865786	12869909	Subtract 2111924
chrY	14981842	14986718	chrY	12869910	12874786	Subtract 2111932
chrY	14986721	14989218	chrY	12874787	12877284	Subtract 2111934
chrY	14989219	15011301	chrY	12877304	12899386	Subtract 2111915
chrY	15011302	15015255	chrY	12899390	12903343	Subtract 2111912
chrY	15015256	15022824	chrY	12903345	12910913	Subtract 2111911
chrY	15022826	15037754	chrY	12910914	12925842	Subtract 2111912
chrY	15037755	15047299	chrY	12925845	12935389	Subtract 2111910
chrY	15047300	15055137	chrY	12935391	12943228	Subtract 2111909
chrY	15055138	15066205	chrY	12943230	12954297	Subtract 2111908
chrY	15066207	15072595	chrY	12954298	12960686	Subtract 2111909
chrY	15072597	15088608	chrY	12960687	12976698	Subtract 2111910
chrY	15088610	15092756	chrY	12976699	12980845	Subtract 2111911
chrY	15092758	15106783	chrY	12980846	12994871	Subtract 2111912
chrY	15106785	15157860	chrY	12994872	13045947	Subtract 2111913
chrY	15157862	15255769	chrY	13045948	13143855	Subtract 2111914
chrY	15255772	15263356	chrY	13143856	13151440	Subtract 2111916
chrY	15263357	15264729	chrY	13151447	13152819	Subtract 2111910
chrY	15264731	15278820	chrY	13152820	13166909	Subtract 2111911
chrY	15278822	15305843	chrY	13166921	13193942	Subtract 2111901
chrY	15305844	15308826	chrY	13193946	13196928	Subtract 2111898
chrY	15308827	15309739	chrY	13196931	13197843	Subtract 2111896
chrY	15309740	15315461	chrY	13197845	13203566	Subtract 2111895
chrY	15315462	15320664	chrY	13203568	13208770	Subtract 2111894
chrY	15320665	15340383	chrY	13208783	13228501	Subtract 2111882
chrY	15340384	15358761	chrY	13228503	13246880	Subtract 2111881
chrY	15358762	20143882	chrY	13246882	18032002	Subtract 2111880
chrY	20193889	22369679	chrY	18032003	20207793	Subtract 2161886
chrY	22419680	23901428	chrY	20257794	21739542	Subtract 2161886
chrY	23951429	28819361	chrY	21805282	26673214	Subtract 2146147
chrY	58819362	58917656	chrY	56771509	56673215	Shift and Reverse Complement
chrY	58967657	59052824	chrY	56821510	56906677	Subtract 2146147
chrY	59052826	59131404	chrY	56906678	56985256	Subtract 2146148
chrY	59131406	59194901	chrY	56985257	57048752	Subtract 2146149
chrY	59194903	59198059	chrY	57048753	57051909	Subtract 2146150
chrY	59198060	59228441	chrY	57051911	57082292	Subtract 2146149
chrY	59228443	59282590	chrY	57082293	57136440	Subtract 2146150
chrY	59282592	59363566	chrY	57136441	57217415	Subtract 2146151

chrY to chrX

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

hg19	hg19 Start	hg19 End	hg38	hg38 Start	hg38 End	Change
chrY	1053477	1056575	chrX	1080362	1083460	Add 26885
chrY	1056595	1056773	chrX	1083478	1083656	Add 26883
chrY	1056822	1056893	chrX	1083705	1083776	Add 26883
chrY	1056942	1056994	chrX	1083826	1083878	Add 26884
chrY	1056995	1057054	chrX	1083938	1083997	Add 26943
chrY	1057061	1057080	chrX	1084004	1084023	Add 26943
chrY	1057081	1057583	chrX	1084498	1085000	Add 27417
chrY	1058695	1058989	chrX	1086261	1086555	Add 27566
chrY	1059359	1059440	chrX	1086040	1086121	Add 26681
chrY	1059767	1059872	chrX	1086153	1086258	Add 26386
chrY	1060044	1060169	chrX	1086430	1086555	Add 26386
chrY	1134114	1134395	chrX	1084845	1085126	Subtract 49269
chrY	1134399	1135088	chrX	1085131	1085820	Subtract 49268
chrY	1135098	1135360	chrX	1085830	1086092	Subtract 49268
chrY	1135361	1135402	chrX	1086388	1086429	Subtract 48973
chrY	1135404	1135444	chrX	1085841	1085881	Subtract 49563
chrY	1135445	1135924	chrX	1086177	1086656	Subtract 49268
chrY	1135925	1136192	chrX	1086067	1086334	Subtract 49858
chrY	1136193	1136219	chrX	1086630	1086656	Subtract 49563
chrY	1136247	1136487	chrX	1086389	1086629	Subtract 49858
chrY	1136783	1136809	chrX	1086040	1086066	Subtract 50743
chrY	1266337	1266396	chrX	1198156	1198215	Subtract 68181
chrY	1266401	1266536	chrX	1198216	1198351	Subtract 68185
chrY	1266563	1266609	chrX	1198378	1198424	Subtract 68185
chrY	1266610	1266641	chrX	1198241	1198272	Subtract 68369
chrY	1266642	1266669	chrX	1198213	1198240	Subtract 68429
chrY	1266670	1266734	chrX	1198425	1198489	Subtract 68245
chrY	1266735	1266761	chrX	1198246	1198272	Subtract 68489

chrX to chrY

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

hg19	hg19 Start	hg19 End	hg38	hg38 Start	hg38 End	Change
chrX	1108695	1108989	chrY	1086261	1086555	Subtract 22434
chrX	1185361	1185402	chrY	1086388	1086429	Subtract 98973
chrX	1185404	1185444	chrY	1085841	1085881	Subtract 99563
chrX	1185925	1186192	chrY	1086067	1086334	Subtract 99858
chrX	1186220	1186246	chrY	1086067	1086093	Subtract 100153
chrX	1186247	1186487	chrY	1086389	1086629	Subtract 99858
chrX	1186570	1186782	chrY	1086122	1086334	Subtract 100448
chrX	1186783	1186809	chrY	1086040	1086066	Subtract 100743
chrX	1316337	1316396	chrY	1198156	1198215	Subtract 118181
chrX	1316401	1316536	chrY	1198216	1198351	Subtract 118185
chrX	1316563	1316609	chrY	1198378	1198424	Subtract 118185
chrX	1316670	1316734	chrY	1198425	1198489	Subtract 118245
chrX	1316790	1317005	chrY	1198181	1198396	Subtract 118609
chrX	115148083	115148144	chrY	14956678	14956617	Shift and Reverse Complement