Skip to content

Instantly share code, notes, and snippets.

@leipzig
Created Jul 31, 2013
Embed
What would you like to do?
hg19 gaps
#bin chrom chromStart chromEnd ix n size type bridge
0 chr1 124535434 142535434 1271 N 18000000 heterochromatin no
23 chr1 121535434 124535434 1270 N 3000000 centromere no
76 chr1 3845268 3995268 47 N 150000 contig no
85 chr1 13219912 13319912 154 N 100000 contig no
89 chr1 17125658 17175658 196 N 50000 clone yes
101 chr1 29878082 30028082 337 N 150000 contig no
188 chr1 120697156 120747156 1263 N 50000 clone yes
188 chr1 120936695 121086695 1265 N 150000 contig no
188 chr1 121485434 121535434 1269 N 50000 clone no
209 chr1 142731022 142781022 1273 N 50000 clone yes
209 chr1 142967761 143117761 1275 N 150000 contig no
210 chr1 143771002 143871002 1281 N 100000 contig no
210 chr1 144401744 144451744 1289 N 50000 clone yes
212 chr1 146253299 146303299 1312 N 50000 clone yes
214 chr1 148026038 148176038 1328 N 150000 contig no
214 chr1 148361358 148511358 1331 N 150000 contig no
269 chr1 205922707 206072707 1875 N 150000 contig no
269 chr1 206332221 206482221 1878 N 150000 contig no
310 chr1 248908210 249058210 2293 N 150000 contig no
585 chr1 0 10000 1 N 10000 telomere no
586 chr1 177417 227417 4 N 50000 clone yes
587 chr1 267719 317719 6 N 50000 contig no
588 chr1 471368 521368 8 N 50000 contig no
605 chr1 2634220 2684220 32 N 50000 clone yes
684 chr1 13052998 13102998 151 N 50000 clone yes
688 chr1 13557162 13607162 157 N 50000 clone yes
1377 chr1 103863906 103913906 1088 N 50000 clone yes
1678 chr1 143292816 143342816 1277 N 50000 clone yes
1680 chr1 143544525 143644525 1279 N 100000 contig no
1684 chr1 144095783 144145783 1285 N 50000 contig no
1685 chr1 144224481 144274481 1287 N 50000 contig no
1688 chr1 144622413 144672413 1291 N 50000 contig no
1689 chr1 144710724 144810724 1293 N 100000 clone yes
1697 chr1 145833118 145883118 1307 N 50000 clone yes
1700 chr1 146164650 146214650 1310 N 50000 clone yes
1719 chr1 148684147 148734147 1333 N 50000 clone yes
1721 chr1 148954460 149004460 1337 N 50000 clone yes
1725 chr1 149459645 149509645 1342 N 50000 clone yes
2292 chr1 223747846 223797846 2038 N 50000 clone yes
2379 chr1 235192211 235242211 2159 N 50000 clone yes
2486 chr1 249240621 249250621 2302 N 10000 telomere no
19 chr2 90545103 91545103 762 N 1000000 heterochromatin no
20 chr2 92326171 95326171 770 N 3000000 centromere no
76 chr2 3529312 3579312 38 N 50000 contig no
77 chr2 5018788 5118788 52 N 100000 contig no
156 chr2 87668206 87718206 739 N 50000 clone yes
158 chr2 89630436 89830436 755 N 200000 contig no
178 chr2 110109337 110251337 893 N 142000 contig no
304 chr2 243102476 243152476 2025 N 50000 clone yes
585 chr2 0 10000 1 N 10000 telomere no
709 chr2 16279724 16329724 149 N 50000 contig no
746 chr2 21153113 21178113 192 N 25000 contig no
1274 chr2 90321525 90371525 760 N 50000 clone yes
1283 chr2 91545103 91595103 763 N 50000 clone no
1727 chr2 149690582 149790582 1221 N 100000 contig no
2370 chr2 234003741 234053741 1942 N 50000 contig no
2414 chr2 239801978 239831978 1992 N 30000 contig no
2422 chr2 240784132 240809132 2001 N 25000 contig no
2440 chr2 243189373 243199373 2027 N 10000 telomere no
2 chr3 90504854 93504854 784 N 3000000 centromere no
136 chr3 66170270 66270270 565 N 100000 contig no
585 chr3 0 10000 1 N 10000 telomere no
585 chr3 10000 60000 2 N 50000 clone no
2065 chr3 194041961 194047251 1693 N 5290 contig no
2095 chr3 197962430 198012430 1732 N 50000 contig no
2095 chr3 198012430 198022430 1733 N 10000 telomere no
1 chr4 49660117 52660117 447 N 3000000 centromere no
16 chr4 59739333 59789333 510 N 50000 contig no
74 chr4 1423146 1478646 15 N 55500 contig no
81 chr4 9274642 9324642 88 N 50000 clone yes
120 chr4 49338941 49488941 445 N 150000 contig no
255 chr4 191044276 191144276 1657 N 100000 clone no
585 chr4 0 10000 1 N 10000 telomere no
652 chr4 8799203 8818203 83 N 19000 contig no
827 chr4 31820917 31837417 283 N 16500 contig no
835 chr4 32834638 32840638 294 N 6000 contig no
892 chr4 40296396 40297096 365 N 700 contig no
1160 chr4 75427379 75452279 651 N 24900 contig no
2043 chr4 191144276 191154276 1658 N 10000 telomere no
14 chr5 46405641 49405641 452 N 3000000 centromere no
89 chr5 17530657 17580657 171 N 50000 clone yes
205 chr5 138787073 138837073 1350 N 50000 contig no
585 chr5 0 10000 1 N 10000 telomere no
1284 chr5 91636128 91686128 873 N 50000 contig no
1768 chr5 155138727 155188727 1514 N 50000 contig no
1965 chr5 180905260 180915260 1775 N 10000 telomere no
585 chr6 0 10000 1 N 10000 telomere no
585 chr6 10000 60000 2 N 50000 contig no
1028 chr6 58087659 58137659 620 N 50000 clone yes
1033 chr6 58780166 58830166 627 N 50000 clone no
16 chr6 58830166 61830166 628 N 3000000 centromere no
16 chr6 61830166 61880166 629 N 50000 clone no
1059 chr6 62128589 62178589 633 N 50000 clone yes
164 chr6 95680543 95830543 992 N 150000 contig no
1787 chr6 157559467 157609467 1652 N 50000 clone yes
223 chr6 157641300 157691300 1654 N 50000 clone yes
233 chr6 167942073 168042073 1761 N 100000 clone yes
1884 chr6 170279972 170329972 1787 N 50000 clone yes
1890 chr6 171055067 171105067 1797 N 50000 contig no
1890 chr6 171105067 171115067 1798 N 10000 telomere no
1 chr7 58054331 61054331 564 N 3000000 centromere no
73 chr7 232484 282484 5 N 50000 clone yes
131 chr7 61310513 61360513 569 N 50000 heterochromatin no
131 chr7 61460465 61510465 571 N 50000 clone yes
208 chr7 142048195 142098195 1397 N 50000 clone yes
209 chr7 143347897 143397897 1409 N 50000 clone yes
220 chr7 154270634 154370634 1517 N 100000 contig no
585 chr7 0 10000 1 N 10000 telomere no
969 chr7 50370631 50410631 488 N 40000 contig no
1055 chr7 61677020 61727020 573 N 50000 clone yes
1057 chr7 61917157 61967157 575 N 50000 heterochromatin no
1155 chr7 74715724 74765724 693 N 50000 clone yes
1352 chr7 100556043 100606043 952 N 50000 clone yes
1578 chr7 130154523 130254523 1278 N 100000 clone yes
1648 chr7 139379377 139404377 1368 N 25000 contig no
1670 chr7 142276197 142326197 1399 N 50000 clone yes
1799 chr7 159128663 159138663 1563 N 10000 telomere no
14 chr8 43838887 46838887 376 N 3000000 centromere no
155 chr8 86576451 86726451 716 N 150000 contig no
211 chr8 145332588 145432588 1209 N 100000 contig no
585 chr8 0 10000 1 N 10000 telomere no
642 chr8 7474649 7524649 66 N 50000 contig no
677 chr8 12091854 12141854 105 N 50000 contig no
952 chr8 48130499 48135599 389 N 5100 contig no
1674 chr8 142766515 142816515 1177 N 50000 clone yes
1701 chr8 146304022 146354022 1216 N 50000 contig no
1701 chr8 146354022 146364022 1217 N 10000 telomere no
585 chr9 0 10000 1 N 10000 telomere no
887 chr9 39663686 39713686 343 N 50000 clone yes
111 chr9 39974796 40024796 346 N 50000 contig no
111 chr9 40233029 40283029 348 N 50000 clone yes
893 chr9 40425834 40475834 350 N 50000 contig no
897 chr9 40940341 40990341 354 N 50000 contig no
112 chr9 41143214 41193214 357 N 50000 clone yes
900 chr9 41365793 41415793 359 N 50000 contig no
910 chr9 42613955 42663955 370 N 50000 contig no
114 chr9 43213698 43313698 375 N 100000 contig no
920 chr9 43946569 43996569 381 N 50000 clone yes
115 chr9 44676646 44726646 386 N 50000 clone yes
115 chr9 44908293 44958293 388 N 50000 clone yes
930 chr9 45250203 45350203 391 N 100000 contig no
934 chr9 45815521 45865521 397 N 50000 contig no
937 chr9 46216430 46266430 400 N 50000 clone yes
117 chr9 46461039 46561039 403 N 100000 contig no
944 chr9 47060133 47160133 408 N 100000 contig no
946 chr9 47317679 47367679 410 N 50000 clone no
1 chr9 47367679 50367679 411 N 3000000 centromere no
1 chr9 50367679 65367679 412 N 15000000 heterochromatin no
135 chr9 65367679 65467679 413 N 100000 contig no
135 chr9 65918360 65968360 418 N 50000 contig no
1090 chr9 66192215 66242215 421 N 50000 clone yes
136 chr9 66404656 66454656 423 N 50000 clone yes
1093 chr9 66614195 66664195 425 N 50000 clone yes
1095 chr9 66863343 66913343 428 N 50000 clone yes
0 chr9 67107834 67207834 430 N 100000 contig no
137 chr9 67366296 67516296 432 N 150000 contig no
137 chr9 67987998 68137998 437 N 150000 contig no
138 chr9 68514181 68664181 441 N 150000 contig no
138 chr9 68838946 68988946 443 N 150000 contig no
1113 chr9 69278385 69328385 446 N 50000 clone yes
1119 chr9 70010542 70060542 452 N 50000 clone yes
17 chr9 70218729 70318729 454 N 100000 contig no
140 chr9 70506535 70556535 456 N 50000 contig no
140 chr9 70735468 70835468 458 N 100000 contig no
161 chr9 92343416 92443416 641 N 100000 clone yes
161 chr9 92528796 92678796 643 N 150000 clone yes
24 chr9 133073060 133223060 982 N 150000 contig no
1630 chr9 137041193 137091193 1020 N 50000 contig no
205 chr9 139166997 139216997 1040 N 50000 contig no
207 chr9 141153431 141203431 1057 N 50000 contig no
1662 chr9 141203431 141213431 1058 N 10000 telomere no
585 chrX 0 10000 1 N 10000 telomere no
585 chrX 10000 60000 2 N 50000 contig no
73 chrX 94821 144821 4 N 50000 contig no
73 chrX 231384 281384 8 N 50000 contig no
9 chrX 1047557 1097557 16 N 50000 contig no
74 chrX 1134113 1184113 18 N 50000 contig no
74 chrX 1264234 1314234 21 N 50000 contig no
9 chrX 2068238 2118238 31 N 50000 contig no
643 chrX 7623882 7673882 82 N 50000 clone yes
83 chrX 10738674 10788674 111 N 50000 clone yes
868 chrX 37098256 37148256 355 N 50000 contig no
14 chrX 49242997 49292997 484 N 50000 contig no
966 chrX 49974173 50024173 494 N 50000 contig no
15 chrX 52395914 52445914 518 N 50000 contig no
128 chrX 58582012 58632012 582 N 50000 clone no
1 chrX 58632012 61632012 583 N 3000000 centromere no
1055 chrX 61632012 61682012 584 N 50000 clone no
146 chrX 76653692 76703692 724 N 50000 contig no
1451 chrX 113517668 113567668 1183 N 50000 contig no
1467 chrX 115682290 115732290 1214 N 50000 contig no
187 chrX 120013235 120063235 1268 N 50000 clone yes
209 chrX 143507324 143557324 1536 N 50000 contig no
1721 chrX 148906424 148956424 1591 N 50000 clone yes
1722 chrX 149032062 149082062 1594 N 50000 contig no
218 chrX 152277099 152327099 1624 N 50000 clone yes
1769 chrX 155260560 155270560 1668 N 10000 telomere no
585 chrY 0 10000 1 N 10000 telomere no
585 chrY 44821 94821 3 N 50000 contig no
586 chrY 181384 231384 7 N 50000 contig no
592 chrY 997557 1047557 15 N 50000 contig no
593 chrY 1084113 1134113 17 N 50000 contig no
594 chrY 1214234 1264234 20 N 50000 contig no
600 chrY 2018238 2068238 30 N 50000 contig no
653 chrY 8914955 8964955 92 N 50000 contig no
655 chrY 9241322 9291322 97 N 50000 contig no
10 chrY 10104553 13104553 105 N 3000000 centromere no
685 chrY 13143954 13193954 107 N 50000 contig no
86 chrY 13748578 13798578 112 N 50000 contig no
92 chrY 20143885 20193885 169 N 50000 clone yes
94 chrY 22369679 22419679 190 N 50000 clone yes
767 chrY 23901428 23951428 204 N 50000 contig no
1 chrY 28819361 58819361 249 N 30000000 heterochromatin no
1034 chrY 58917656 58967656 251 N 50000 contig no
1037 chrY 59363566 59373566 255 N 10000 telomere no
1 chr10 39254935 42254935 341 N 3000000 centromere no
110 chr10 39154935 39254935 340 N 100000 contig no
113 chr10 42254935 42354935 342 N 100000 contig no
118 chr10 47429169 47529169 387 N 100000 contig no
118 chr10 47792476 47892476 390 N 100000 contig no
118 chr10 48055707 48105707 392 N 50000 contig no
119 chr10 49095536 49195536 403 N 100000 contig no
195 chr10 128616069 128766069 1088 N 150000 contig no
200 chr10 133381404 133431404 1129 N 50000 clone yes
200 chr10 133677527 133727527 1135 N 50000 clone yes
202 chr10 135524747 135534747 1156 N 10000 telomere no
585 chr10 0 10000 1 N 10000 telomere no
585 chr10 10000 60000 2 N 50000 contig no
722 chr10 17974675 18024675 161 N 50000 clone yes
881 chr10 38818835 38868835 337 N 50000 clone yes
909 chr10 42546687 42596687 344 N 50000 clone yes
939 chr10 46426964 46476964 375 N 50000 contig no
975 chr10 51137410 51187410 419 N 50000 clone yes
977 chr10 51398845 51448845 421 N 50000 clone yes
1545 chr10 125869472 125919472 1061 N 50000 clone yes
15 chr11 51644205 54644205 447 N 3000000 centromere no
74 chr11 1162759 1212759 14 N 50000 clone yes
121 chr11 50833853 51040853 440 N 207000 heterochromatin no
122 chr11 51594205 51644205 446 N 50000 clone no
125 chr11 54644205 54694205 448 N 50000 clone no
139 chr11 69724695 69774695 583 N 50000 clone yes
164 chr11 96287584 96437584 808 N 150000 contig no
201 chr11 134996516 135006516 1135 N 10000 telomere no
585 chr11 0 10000 1 N 10000 telomere no
585 chr11 10000 60000 2 N 50000 contig no
972 chr11 50783853 50833853 439 N 50000 clone no
974 chr11 51040853 51090853 441 N 50000 clone no
1112 chr11 69089801 69139801 575 N 50000 clone yes
1254 chr11 87688378 87738378 736 N 50000 clone yes
1614 chr11 134946516 134996516 1134 N 50000 contig no
585 chr12 0 10000 1 N 10000 telomere no
585 chr12 10000 60000 2 N 50000 contig no
73 chr12 95739 145739 4 N 50000 clone yes
79 chr12 7189876 7239876 66 N 50000 contig no
13 chr12 34856694 37856694 304 N 3000000 centromere no
1419 chr12 109373470 109423470 954 N 50000 contig no
189 chr12 122530623 122580623 1075 N 50000 contig no
199 chr12 132706992 132806992 1171 N 100000 contig no
1606 chr12 133841895 133851895 1183 N 10000 telomere no
1 chr13 10000 16000000 2 N 15990000 short_arm no
1 chr13 16000000 19000000 3 N 3000000 centromere no
91 chr13 19000000 19020000 4 N 20000 heterochromatin no
155 chr13 86760324 86910324 617 N 150000 contig no
180 chr13 112353994 112503994 848 N 150000 contig no
182 chr13 114325993 114425993 866 N 100000 contig no
182 chr13 114639948 114739948 870 N 100000 contig no
585 chr13 0 10000 1 N 10000 telomere no
1463 chr13 115109878 115159878 875 N 50000 contig no
1463 chr13 115159878 115169878 876 N 10000 telomere no
585 chr14 0 10000 1 N 10000 telomere no
1 chr14 10000 16000000 2 N 15990000 short_arm no
1 chr14 16000000 19000000 3 N 3000000 centromere no
1403 chr14 107289540 107339540 667 N 50000 contig no
175 chr14 107339540 107349540 668 N 10000 telomere no
1 chr15 10000 17000000 2 N 16990000 short_arm no
11 chr15 17000000 20000000 3 N 3000000 centromere no
18 chr15 82829645 82879645 518 N 50000 contig no
93 chr15 21398819 21885000 16 N 486181 clone yes
585 chr15 0 10000 1 N 10000 telomere no
744 chr15 20894633 20935075 12 N 40442 clone yes
754 chr15 22212114 22262114 19 N 50000 contig no
757 chr15 22596193 22646193 23 N 50000 contig no
764 chr15 23514853 23564853 31 N 50000 contig no
807 chr15 29159443 29209443 83 N 50000 contig no
1233 chr15 84984473 85034473 539 N 50000 contig no
1367 chr15 102521392 102531392 690 N 10000 telomere no
1 chr16 38335801 46335801 355 N 8000000 heterochromatin no
13 chr16 35335801 38335801 354 N 3000000 centromere no
81 chr16 8636921 8686921 128 N 50000 clone yes
105 chr16 34023150 34173150 343 N 150000 contig no
159 chr16 90294753 90344753 731 N 50000 contig no
585 chr16 0 10000 1 N 10000 telomere no
585 chr16 10000 60000 2 N 50000 contig no
854 chr16 35285801 35335801 353 N 50000 clone no
938 chr16 46335801 46385801 356 N 50000 clone no
1259 chr16 88389383 88439383 712 N 50000 contig no
1274 chr16 90344753 90354753 732 N 10000 telomere no
1 chr17 22263006 25263006 192 N 3000000 centromere no
18 chr17 77546461 77596461 644 N 50000 clone yes
73 chr17 296626 396626 4 N 100000 contig no
93 chr17 21566608 21666608 185 N 100000 contig no
849 chr17 34675848 34725848 278 N 50000 contig no
1061 chr17 62410760 62460760 523 N 50000 clone yes
1193 chr17 79709049 79759049 665 N 50000 contig no
1 chr18 15460898 18460898 125 N 3000000 centromere no
90 chr18 18460898 18510898 126 N 50000 clone no
122 chr18 52059136 52209136 398 N 150000 contig no
145 chr18 75721820 75771820 585 N 50000 clone yes
585 chr18 0 10000 1 N 10000 telomere no
702 chr18 15410898 15460898 124 N 50000 clone no
1136 chr18 72283353 72333353 555 N 50000 clone yes
1180 chr18 78017248 78067248 604 N 50000 contig no
1180 chr18 78067248 78077248 605 N 10000 telomere no
585 chr19 0 10000 1 N 10000 telomere no
585 chr19 10000 60000 2 N 50000 contig no
641 chr19 7346004 7396004 170 N 50000 contig no
651 chr19 8687198 8737198 190 N 50000 contig no
741 chr19 20523415 20573415 367 N 50000 clone yes
96 chr19 24631782 24681782 409 N 50000 heterochromatin no
1 chr19 24681782 27681782 410 N 3000000 centromere no
796 chr19 27681782 27731782 411 N 50000 heterochromatin no
1036 chr19 59118983 59128983 870 N 10000 telomere no
585 chr20 0 10000 1 N 10000 telomere no
585 chr20 10000 60000 2 N 50000 contig no
98 chr20 26319569 26369569 274 N 50000 clone no
12 chr20 26369569 29369569 275 N 3000000 centromere no
809 chr20 29369569 29419569 276 N 50000 clone no
101 chr20 29653908 29803908 279 N 150000 contig no
851 chr20 34897085 34947085 336 N 50000 clone yes
1051 chr20 61091437 61141437 624 N 50000 clone yes
1052 chr20 61213369 61263369 628 N 50000 contig no
1065 chr20 62965520 63015520 648 N 50000 contig no
1065 chr20 63015520 63025520 649 N 10000 telomere no
1 chr21 5211193 9411193 3 N 4200000 contig no
9 chr21 10000 5211193 2 N 5201193 short_arm no
10 chr21 11288129 14288129 22 N 3000000 centromere no
14 chr21 42955559 43005559 419 N 50000 contig no
82 chr21 10215976 10365976 12 N 150000 contig no
83 chr21 11238129 11288129 21 N 50000 heterochromatin no
585 chr21 0 10000 1 N 10000 telomere no
658 chr21 9595548 9645548 5 N 50000 contig no
659 chr21 9775437 9825437 7 N 50000 contig no
661 chr21 10034920 10084920 10 N 50000 contig no
666 chr21 10647896 10697896 15 N 50000 contig no
670 chr21 11188129 11238129 20 N 50000 clone no
694 chr21 14288129 14338129 23 N 50000 clone no
925 chr21 44632664 44682664 447 N 50000 clone yes
952 chr21 48119895 48129895 515 N 10000 telomere no
585 chr22 0 10000 1 N 10000 telomere no
1 chr22 10000 13000000 2 N 12990000 short_arm no
10 chr22 13000000 16000000 3 N 3000000 centromere no
707 chr22 16000000 16050000 4 N 50000 contig no
1 chr22 16697850 16847850 27 N 150000 contig no
92 chr22 20509431 20609431 81 N 100000 contig no
969 chr22 50364777 50414777 563 N 50000 contig no
121 chr22 51244566 51294566 591 N 50000 contig no
976 chr22 51294566 51304566 592 N 10000 telomere no
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment