hg19ToHg38.over.chain.gz

[Jai Vk (Portbo)]

Hi,

I noticed that the chain file has some gaps leading to unmapped regions.

For example

17:36610408 (GRCh38)

17:34966847 (GRCh37)

The hg19 position is missing from the chain file and hence not mapped:

zcat hg19ToHg38.over.chain.gz | grep "^chain" | grep "chr17"            
chain 7933 chr14 107349540 + 106568871 106569024 chr17 83257441 + 14603055 14603209 24252735
chain 1743 chr14 107349540 + 23106423 23106449 chr17 83257441 + 2447796 2447822 686431
chain 7373267797 chr17 81195210 + 0 81195210 chr17 83257441 + 150207 83247441 18
chain 5812699 chr17 81195210 + 34511469 34747565 chr17_KI270909v1_alt 325800 + 138204 310827 209
chain 2078860 chr17 81195210 + 21532757 21564472 chr17 83257441 - 61183645 61215380 1437
chain 1335341 chr17 81195210 + 77614970 77628903 chr17 83257441 + 79517567 79531500 2966
chain 585722 chr17 81195210 + 34376281 36546159 chr17_KI270857v1_alt 2877074 + 283809 2425225 78
chain 479136 chr17 81195210 + 77601352 77606352 chr17 83257441 + 79504000 79509000 51486
chain 429458 chr17 81195210 + 77596852 77601352 chr17 83257441 + 79499500 79504000 53526
chain 422990 chr17 81195210 + 77606352 77610902 chr17 83257441 + 79509000 79513500 63462
chain 390235 chr17 81195210 + 77610902 77614969 chr17 83257441 + 79513500 79517567 94814
chain 154348 chr17 81195210 + 77628903 77630507 chr17 83257441 + 79531500 79533104 589049
chain 58462 chr17 81195210 + 1020324 1057040 chr17_KI270862v1_alt 391357 + 160633 197561 186
chain 34692 chr17 81195210 + 77596487 77596852 chr17 83257441 + 79499135 79499500 1798535
chain 19822 chr17 81195210 + 34796308 34797394 chr17 83257441 + 36164817 36165903 2731
chain 19410 chr17 81195210 + 34675022 34675848 chr17 83257441 + 37970530 37971356 1295
chain 5679 chr17 81195210 + 1024821 1024880 chr17_KI270862v1_alt 391357 + 165696 165755 9871921
chain 5628 chr17 81195210 + 1020501 1020739 chr17_KI270862v1_alt 391357 + 161389 162205 4334829
chain 5534 chr17 81195210 + 1056808 1056982 chr17 83257441 + 1153544 1153660 4507314
chain 4913 chr17 81195210 + 81048174 81048227 chr17_KI270860v1_alt 178921 - 165413 165450 388
chain 4218 chr17 81195210 + 81058474 81058598 chr17 83257441 + 83100775 83100850 35360840
chain 3350 chr17 81195210 + 77675126 77675171 chr17 83257441 + 79701206 79701251 24078543
chain 3199 chr17 81195210 + 34814368 34814404 chr17_KI270857v1_alt 2877074 - 720500 720536 2341
chain 2507 chr17 81195210 + 77610080 77610118 chr17 83257441 + 79513028 79513066 23510665
chain 1425 chr17 81195210 + 77610031 77610061 chr17 83257441 + 79512629 79512659 24069512
chain 1401 chr17 81195210 + 1022421 1022450 chr17_KI270862v1_alt 391357 + 163026 163055 1974124
chain 1153 chr17 81195210 + 34795643 34810476 chr17 83257441 - 45320543 45335398 1396
chain 1008 chr17 81195210 + 34797737 34808196 chr17_KI270857v1_alt 2877074 + 489109 499567 908
chain 922 chr17 81195210 + 81058722 81058751 chr17 83257441 + 83100684 83100713 29503291
chain 722 chr17 81195210 + 34750764 34784637 chr17 83257441 - 45326734 45360613 521
chain 149625828 chr17_ctg5_hap1 1680828 + 1999 1680828 chr17_GL000258v2_alt 1821992 + 0 1821992 96
chain 57095 chr17_ctg5_hap1 1680828 + 0 1999 chr17 83257441 + 45307497 45309497 155
chain 9690 chr17_ctg5_hap1 1680828 + 1306794 1306897 chr17_KI270908v1_alt 1423190 - 510330 510433 717801
chain 3499015 chr17_gl000203_random 37498 + 8 37490 chr17 83257441 - 61083795 61125679 1443
chain 7571279 chr17_gl000204_random 81310 + 0 81310 chr17 83257441 + 79466298 79635384 865
chain 15614048 chr17_gl000205_random 174588 + 0 174588 chr17_GL000205v2_random 185591 - 10808 185591 438
chain 550304 chr17_gl000205_random 174588 + 8117 15953 chr21 46709983 + 6292665 6300498 948
chain 49989 chr17_gl000205_random 174588 + 15953 16657 chrUn_GL000195v1 182896 + 120016 120712 1053
chain 3855332 chr17_gl000206_random 41001 + 8 40993 chr17 83257441 + 83162353 83202887 1346
chain 35556 chr17_gl000206_random 41001 + 19273 19640 chr17 83257441 + 83181482 83181849 3375601
chain 8661 chr17_gl000206_random 41001 + 19184 19273 chr17 83257441 + 83181583 83181672 3994518
chain 587 chr9 141213431 + 40369087 40369118 chr17 83257441 + 15506084 15506115 18139865
chain 23035 chrX 155270560 + 114670506 114670787 chr17 83257441 + 58762631 58762912 10104613
chain 5130 chrX 155270560 + 115147876 115147930 chr17 83257441 - 47859510 47859564 26741146
chain 1485 chrX 155270560 + 103324359 103324437 chr17 83257441 + 27099174 27099252 3850783
chain 1362 chrX 155270560 + 114581793 114581816 chr17 83257441 - 22705213 22705236 1315104

But stragely when i use UCSC browser it remaps it correctly to the new position
chr17 36610408 36610408

Can someone comment on why these gaps exist in the chain file and how the UCSC browser is able to map it correctly.

BW,

Jay