Available Genomes:
The genomes below are CC strain specific paths from the Collaborative-Cross Graphical Genome. They are provided as standard FASTA files that are compatible with traditional genomic tools. In addition, we also supply an anchor mapping file for each strain that can be used to map coordinates between various CC-specific genomes and genome reference sequeces. The current genome versions are 0.2 and are considered "Beta" qualitity. All of the genomes offered here have successfully been used for sequence aligments using Bowtie2 and minimap. Additional CC genomes will be included as they are validated.
The resource is funded by the NIH National Human Genome Research Institute under grant number U24HG010100.
CC001
Genome: CC001_Genome.fa.gz (693.00 Mb)Mapping: CC001_anchorinfo.csv (585.00 Mb)
Enter a genomic coordinate or coordinate range to find the CCGG subpath for this strain. The GFF file provides anchor anotations suitable for display in IGV.
| Chromosome | length |
|---|---|
| 1 | 201150004 |
| 2 | 182276701 |
| 3 | 158066608 |
| 4 | 159445038 |
| 5 | 152568998 |
| 6 | 149802450 |
| 7 | 148119586 |
| 8 | 127378187 |
| 9 | 124553577 |
| 10 | 139482669 |
| 11 | 124684237 |
| 12 | 122864139 |
| 13 | 118592622 |
| 14 | 116847031 |
| 15 | 105718276 |
| 16 | 99020741 |
| 17 | 95952349 |
| 18 | 91721189 |
| 19 | 60392525 |
| X | 168184958 |
CC003
Genome: CC003_Genome.fa.gz (688.00 Mb)Mapping: CC003_anchorinfo.csv (582.00 Mb)
Enter a genomic coordinate or coordinate range to find the CCGG subpath for this strain. The GFF file provides anchor anotations suitable for display in IGV.
| Chromosome | length |
|---|---|
| 1 | 203822516 |
| 2 | 182129585 |
| 3 | 157534305 |
| 4 | 158087901 |
| 5 | 155979058 |
| 6 | 152199214 |
| 7 | 147232085 |
| 8 | 134466958 |
| 9 | 122019902 |
| 10 | 134134961 |
| 11 | 122878308 |
| 12 | 120652920 |
| 13 | 122347257 |
| 14 | 121252054 |
| 15 | 103030598 |
| 16 | 105736451 |
| 17 | 99737716 |
| 18 | 87945846 |
| 19 | 59467814 |
| X | 162489431 |
CC004
Genome: CC004_Genome.fa.gz (681.00 Mb)Mapping: CC004_anchorinfo.csv (584.00 Mb)
Enter a genomic coordinate or coordinate range to find the CCGG subpath for this strain. The GFF file provides anchor anotations suitable for display in IGV.
| Chromosome | length |
|---|---|
| 1 | 196209404 |
| 2 | 187311757 |
| 3 | 161889577 |
| 4 | 166662602 |
| 5 | 152428789 |
| 6 | 159598788 |
| 7 | 148493143 |
| 8 | 133116296 |
| 9 | 125947319 |
| 10 | 133997512 |
| 11 | 127180750 |
| 12 | 120065944 |
| 13 | 122446123 |
| 14 | 122583420 |
| 15 | 103854328 |
| 16 | 97618814 |
| 17 | 97947093 |
| 18 | 87831348 |
| 19 | 60354228 |
| X | 168144042 |
CC005
Genome: CC005_Genome.fa.gz (693.00 Mb)Mapping: CC005_anchorinfo.csv (586.00 Mb)
Enter a genomic coordinate or coordinate range to find the CCGG subpath for this strain. The GFF file provides anchor anotations suitable for display in IGV.
| Chromosome | length |
|---|---|
| 1 | 205727657 |
| 2 | 189242119 |
| 3 | 184057662 |
| 4 | 163834966 |
| 5 | 152789772 |
| 6 | 153815254 |
| 7 | 151959071 |
| 8 | 132957138 |
| 9 | 124423868 |
| 10 | 138966901 |
| 11 | 125934458 |
| 12 | 126594243 |
| 13 | 125285421 |
| 14 | 121252094 |
| 15 | 106265831 |
| 16 | 96988083 |
| 17 | 96885033 |
| 18 | 90511607 |
| 19 | 58952666 |
| X | 168370664 |
CC009
Genome: CC009_Genome.fa.gz (700.00 Mb)Mapping: CC009_anchorinfo.csv (546.00 Mb)
Enter a genomic coordinate or coordinate range to find the CCGG subpath for this strain. The GFF file provides anchor anotations suitable for display in IGV.
| Chromosome | length |
|---|---|
| 1 | 203182174 |
| 2 | 187280720 |
| 3 | 160375785 |
| 4 | 159081848 |
| 5 | 155577400 |
| 6 | 158395870 |
| 7 | 152444273 |
| 8 | 130246402 |
| 9 | 124242749 |
| 10 | 130588241 |
| 11 | 126184437 |
| 12 | 122431066 |
| 13 | 120323547 |
| 14 | 123396132 |
| 15 | 111292723 |
| 16 | 102638079 |
| 17 | 98021260 |
| 18 | 90962289 |
| 19 | 63672350 |
| X | 167312164 |
| Y(?) | 91740947 |
| MT(E) | 16339 |
CC010
Genome: CC010_Genome.fa.gz (701.00 Mb)Mapping: CC010_anchorinfo.csv (548.00 Mb)
Enter a genomic coordinate or coordinate range to find the CCGG subpath for this strain. The GFF file provides anchor anotations suitable for display in IGV.
| Chromosome | length |
|---|---|
| 1 | 198293499 |
| 2 | 185967225 |
| 3 | 178971045 |
| 4 | 156234306 |
| 5 | 155916418 |
| 6 | 153181759 |
| 7 | 160238751 |
| 8 | 130371115 |
| 9 | 123007240 |
| 10 | 134108129 |
| 11 | 129926379 |
| 12 | 119194770 |
| 13 | 122300686 |
| 14 | 118414816 |
| 15 | 106557581 |
| 16 | 99225723 |
| 17 | 96508719 |
| 18 | 90611357 |
| 19 | 60320780 |
| X | 175261444 |
| Y(?) | 91740947 |
| MT(A) | 16338 |
CC012
Genome: CC012_Genome.fa.gz (700.00 Mb)Mapping: CC012_anchorinfo.csv (547.00 Mb)
Enter a genomic coordinate or coordinate range to find the CCGG subpath for this strain. The GFF file provides anchor anotations suitable for display in IGV.
| Chromosome | length |
|---|---|
| 1 | 202402230 |
| 2 | 185163533 |
| 3 | 160090466 |
| 4 | 161625613 |
| 5 | 160981404 |
| 6 | 153763636 |
| 7 | 156686487 |
| 8 | 139574334 |
| 9 | 136762099 |
| 10 | 129294003 |
| 11 | 125248899 |
| 12 | 128428380 |
| 13 | 122949769 |
| 14 | 134373104 |
| 15 | 103690816 |
| 16 | 97269424 |
| 17 | 95589468 |
| 18 | 89714158 |
| 19 | 61988271 |
| X | 182293721 |
| Y(?) | 91740947 |
| MT(B) | 16336 |
CC019
Genome: CC019_Genome.fa.gz (703.00 Mb)Mapping: CC019_anchorinfo.csv (548.00 Mb)
Enter a genomic coordinate or coordinate range to find the CCGG subpath for this strain. The GFF file provides anchor anotations suitable for display in IGV.
| Chromosome | length |
|---|---|
| 1 | 197528483 |
| 2 | 183687691 |
| 3 | 160879850 |
| 4 | 160795467 |
| 5 | 159526545 |
| 6 | 153044110 |
| 7 | 147166490 |
| 8 | 133733494 |
| 9 | 126465191 |
| 10 | 134993010 |
| 11 | 124780288 |
| 12 | 121117246 |
| 13 | 122563228 |
| 14 | 121577098 |
| 15 | 104872736 |
| 16 | 96913190 |
| 17 | 98363330 |
| 18 | 89223419 |
| 19 | 60284824 |
| X | 165190013 |
| Y(?) | 91740947 |
| MT(E) | 16340 |
CC025
Genome: CC025_Genome.fa.gz (696.00 Mb)Mapping: CC025_anchorinfo.csv (546.00 Mb)
Enter a genomic coordinate or coordinate range to find the CCGG subpath for this strain. The GFF file provides anchor anotations suitable for display in IGV.
| Chromosome | length |
|---|---|
| 1 | 207655344 |
| 2 | 193342700 |
| 3 | 174777943 |
| 4 | 161286607 |
| 5 | 155378902 |
| 6 | 149555697 |
| 7 | 156735298 |
| 8 | 135160672 |
| 9 | 127356118 |
| 10 | 131742962 |
| 11 | 125567828 |
| 12 | 115565628 |
| 13 | 121739230 |
| 14 | 118430083 |
| 15 | 105212334 |
| 16 | 96551357 |
| 17 | 98700985 |
| 18 | 89430890 |
| 19 | 60974841 |
| X | 165901614 |
| Y(?) | 91740947 |
| MT(F) | 16336 |
CC026
Genome: CC026_Genome.fa.gz (678.00 Mb)Mapping: CC026_anchorinfo.csv (584.00 Mb)
Enter a genomic coordinate or coordinate range to find the CCGG subpath for this strain. The GFF file provides anchor anotations suitable for display in IGV.
| Chromosome | length |
|---|---|
| 1 | 200340454 |
| 2 | 184695209 |
| 3 | 166138287 |
| 4 | 159726732 |
| 5 | 155265744 |
| 6 | 155208188 |
| 7 | 145915165 |
| 8 | 131831087 |
| 9 | 124441261 |
| 10 | 131843873 |
| 11 | 123656838 |
| 12 | 122259365 |
| 13 | 122673930 |
| 14 | 121959660 |
| 15 | 104068707 |
| 16 | 98293040 |
| 17 | 97160476 |
| 18 | 89938449 |
| 19 | 59270637 |
| X | 183153510 |
CC027
Genome: CC027_Genome.fa.gz (699.00 Mb)Mapping: CC027_anchorinfo.csv (547.00 Mb)
Enter a genomic coordinate or coordinate range to find the CCGG subpath for this strain. The GFF file provides anchor anotations suitable for display in IGV.
| Chromosome | length |
|---|---|
| 1 | 209383012 |
| 2 | 182320167 |
| 3 | 158442455 |
| 4 | 166229666 |
| 5 | 152313622 |
| 6 | 157585700 |
| 7 | 150832300 |
| 8 | 137613189 |
| 9 | 126821288 |
| 10 | 134687152 |
| 11 | 122653995 |
| 12 | 123023819 |
| 13 | 122032494 |
| 14 | 119515933 |
| 15 | 103050702 |
| 16 | 99192756 |
| 17 | 99117330 |
| 18 | 96268236 |
| 19 | 61015951 |
| X | 165807066 |
| Y(?) | 91740947 |
| MT(F) | 16336 |
CC028
Genome: CC028_Genome.fa.gz (679.00 Mb)Mapping: CC028_anchorinfo.csv (583.00 Mb)
Enter a genomic coordinate or coordinate range to find the CCGG subpath for this strain. The GFF file provides anchor anotations suitable for display in IGV.
| Chromosome | length |
|---|---|
| 1 | 199988743 |
| 2 | 188200232 |
| 3 | 158105245 |
| 4 | 158909638 |
| 5 | 157430354 |
| 6 | 159554220 |
| 7 | 150874502 |
| 8 | 137076253 |
| 9 | 125223311 |
| 10 | 133573930 |
| 11 | 122320983 |
| 12 | 121046455 |
| 13 | 125486262 |
| 14 | 121991694 |
| 15 | 103942582 |
| 16 | 103235589 |
| 17 | 97280958 |
| 18 | 91079672 |
| 19 | 62271428 |
| X | 180530443 |
CC029
Genome: CC029_Genome.fa.gz (709.00 Mb)Mapping: CC029_anchorinfo.csv (610.00 Mb)
Enter a genomic coordinate or coordinate range to find the CCGG subpath for this strain. The GFF file provides anchor anotations suitable for display in IGV.
| Chromosome | length |
|---|---|
| 1 | 197483018 |
| 2 | 182932490 |
| 3 | 160755826 |
| 4 | 156864066 |
| 5 | 156437270 |
| 6 | 150666585 |
| 7 | 147890478 |
| 8 | 132958389 |
| 9 | 125289303 |
| 10 | 129341623 |
| 11 | 126171694 |
| 12 | 126955871 |
| 13 | 117000448 |
| 14 | 118623563 |
| 15 | 105125041 |
| 16 | 98283922 |
| 17 | 97974536 |
| 18 | 93600308 |
| 19 | 61953665 |
| X | 183407961 |
| Y(?) | 91744698 |
| MT(H) | 16338 |
CC032
Genome: CC032_Genome.fa.gz (708.00 Mb)Mapping: CC032_anchorinfo.csv (547.00 Mb)
Enter a genomic coordinate or coordinate range to find the CCGG subpath for this strain. The GFF file provides anchor anotations suitable for display in IGV.
| Chromosome | length |
|---|---|
| 1 | 194591357 |
| 2 | 186352247 |
| 3 | 160455815 |
| 4 | 155600048 |
| 5 | 151968671 |
| 6 | 151508828 |
| 7 | 147758164 |
| 8 | 131728413 |
| 9 | 125698231 |
| 10 | 129632405 |
| 11 | 127283002 |
| 12 | 114896222 |
| 13 | 117079281 |
| 14 | 122212741 |
| 15 | 103872876 |
| 16 | 96900745 |
| 17 | 96035861 |
| 18 | 87531702 |
| 19 | 60341565 |
| X | 166566796 |
| Y(?) | 91740947 |
| MT(A) | 16338 |
CC035
Genome: CC035_Genome.fa.gz (698.00 Mb)Mapping: CC035_anchorinfo.csv (546.00 Mb)
Enter a genomic coordinate or coordinate range to find the CCGG subpath for this strain. The GFF file provides anchor anotations suitable for display in IGV.
| Chromosome | length |
|---|---|
| 1 | 198675336 |
| 2 | 198349304 |
| 3 | 164145848 |
| 4 | 165047631 |
| 5 | 154127455 |
| 6 | 151466191 |
| 7 | 150834766 |
| 8 | 134026365 |
| 9 | 128659629 |
| 10 | 132490472 |
| 11 | 128695832 |
| 12 | 120763091 |
| 13 | 121098086 |
| 14 | 123464976 |
| 15 | 108376352 |
| 16 | 101384590 |
| 17 | 97954877 |
| 18 | 91068421 |
| 19 | 58707067 |
| X | 173191634 |
| Y(?) | 91740947 |
| MT(F) | 16336 |
CC037
Genome: CC037_Genome.fa.gz (705.00 Mb)Mapping: CC037_anchorinfo.csv (549.00 Mb)
Enter a genomic coordinate or coordinate range to find the CCGG subpath for this strain. The GFF file provides anchor anotations suitable for display in IGV.
| Chromosome | length |
|---|---|
| 1 | 216328180 |
| 2 | 188966445 |
| 3 | 167673018 |
| 4 | 166480156 |
| 5 | 151917465 |
| 6 | 157589529 |
| 7 | 147148926 |
| 8 | 138940526 |
| 9 | 129529972 |
| 10 | 133132282 |
| 11 | 128549410 |
| 12 | 119358241 |
| 13 | 120877833 |
| 14 | 123819338 |
| 15 | 112886892 |
| 16 | 101213863 |
| 17 | 96932259 |
| 18 | 91710704 |
| 19 | 59373433 |
| X | 174689750 |
| Y(?) | 91740947 |
| MT(C) | 16337 |
CC039
Genome: CC039_Genome.fa.gz (704.00 Mb)Mapping: CC039_anchorinfo.csv (607.00 Mb)
Enter a genomic coordinate or coordinate range to find the CCGG subpath for this strain. The GFF file provides anchor anotations suitable for display in IGV.
| Chromosome | length |
|---|---|
| 204270864 | |
| 186312828 | |
| 160273550 | |
| 162959060 | |
| 154364466 | |
| 161561111 | |
| 155245230 | |
| 132120590 | |
| 124761263 | |
| 1 | 131859289 |
| 1 | 125066088 |
| 1 | 121654438 |
| 1 | 120024869 |
| 1 | 121152174 |
| 1 | 114581034 |
| 1 | 98590234 |
| 1 | 95756602 |
| 1 | 90806420 |
| 1 | 62976864 |
| 179760216 | |
| 91744698 | |
| 16337 |
CC040
Genome: CC040_Genome.fa.gz (716.00 Mb)Mapping: CC040_anchorinfo.csv (610.00 Mb)
Enter a genomic coordinate or coordinate range to find the CCGG subpath for this strain. The GFF file provides anchor anotations suitable for display in IGV.
| Chromosome | length |
|---|---|
| 201430855 | |
| 186396615 | |
| 162193528 | |
| 159976406 | |
| 158467409 | |
| 153364657 | |
| 149904583 | |
| 132152841 | |
| 125076619 | |
| 1 | 131763720 |
| 1 | 122329449 |
| 1 | 131880730 |
| 1 | 118588463 |
| 1 | 119753214 |
| 1 | 105815907 |
| 1 | 106884996 |
| 1 | 96155488 |
| 1 | 92405806 |
| 1 | 61113421 |
| 170659374 | |
| 91744698 | |
| 16336 | |
| 16336 |
CC043
Genome: CC043_Genome.fa.gz (700.00 Mb)Mapping: CC043_anchorinfo.csv (547.00 Mb)
Enter a genomic coordinate or coordinate range to find the CCGG subpath for this strain. The GFF file provides anchor anotations suitable for display in IGV.
| Chromosome | length |
|---|---|
| 1 | 200966649 |
| 2 | 197919961 |
| 3 | 169614773 |
| 4 | 165264658 |
| 5 | 155867552 |
| 6 | 149955332 |
| 7 | 143819767 |
| 8 | 131722193 |
| 9 | 129098468 |
| 10 | 136108102 |
| 11 | 123888794 |
| 12 | 130453836 |
| 13 | 126351252 |
| 14 | 115261096 |
| 15 | 109506350 |
| 16 | 102191023 |
| 17 | 101324346 |
| 18 | 90563337 |
| 19 | 60978301 |
| X | 171715105 |
| Y(?) | 91740947 |
| MT(B) | 16336 |
CC049
Genome: CC049_Genome.fa.gz (715.00 Mb)Mapping: CC049_anchorinfo.csv (610.00 Mb)
Enter a genomic coordinate or coordinate range to find the CCGG subpath for this strain. The GFF file provides anchor anotations suitable for display in IGV.
CC059
Genome: CC059_Genome.fa.gz (717.00 Mb)CC060
Genome: CC060_Genome.fa.gz (705.00 Mb)Mapping: CC060_anchorinfo.csv (612.00 Mb)
Enter a genomic coordinate or coordinate range to find the CCGG subpath for this strain. The GFF file provides anchor anotations suitable for display in IGV.
CC061
Genome: CC061_Genome.fa.gz (708.00 Mb)Mapping: CC061_anchorinfo.csv (547.00 Mb)
Enter a genomic coordinate or coordinate range to find the CCGG subpath for this strain. The GFF file provides anchor anotations suitable for display in IGV.
| Chromosome | length |
|---|---|
| 1 | 194046343 |
| 2 | 181885799 |
| 3 | 158871734 |
| 4 | 154566974 |
| 5 | 152961432 |
| 6 | 155652191 |
| 7 | 150714610 |
| 8 | 131070374 |
| 9 | 123348276 |
| 10 | 130731796 |
| 11 | 123545240 |
| 12 | 123330002 |
| 13 | 129469486 |
| 14 | 121439993 |
| 15 | 108396493 |
| 16 | 98052913 |
| 17 | 101919334 |
| 18 | 90555688 |
| 19 | 61850048 |
| X | 168277658 |
| Y(?) | 91740947 |
| MT(D) | 16338 |
CC072
Genome: CC072_Genome.fa.gz (712.00 Mb)Mapping: CC072_anchorinfo.csv (550.00 Mb)
Enter a genomic coordinate or coordinate range to find the CCGG subpath for this strain. The GFF file provides anchor anotations suitable for display in IGV.
| Chromosome | length |
|---|---|
| 1 | 201047948 |
| 2 | 195161972 |
| 3 | 160039681 |
| 4 | 155806722 |
| 5 | 161475306 |
| 6 | 153835757 |
| 7 | 145446983 |
| 8 | 128556001 |
| 9 | 124985564 |
| 10 | 141395814 |
| 11 | 127420130 |
| 12 | 133085641 |
| 13 | 121043883 |
| 14 | 126117341 |
| 15 | 106642480 |
| 16 | 96309587 |
| 17 | 95476850 |
| 18 | 96725430 |
| 19 | 65501571 |
| X | 183118188 |
| Y(?) | 91740947 |
| MT(A) | 16338 |