UNC Systems Genetics

Collaborative Cross Genomes

On this page we provide full genomic sequences for the Collaborative Cross (CC) mouse strains in the form of FASTA files for the 19 autosomes, sex chromosomes (X and Y), and mitochondria (M). They can be used as reference sequences for high-throughput short-read alignments, or for any other comparative genomic analyses.

Each genome comes with a companion MOD file, which can be used to remap coordinates from the FASTA sequences back to reference coordinates (Currently NCBI37/mm9). This is essential since all gene and genomic annotations are relative to the reference. MOD files are genome and version specific, and therefore should always be downloaded together as a set.

We supply two types of genomes, sequenced and imputed. Sequenced genomes result from direct DNA sequencing at a minimum of 30x coverage, and an iterative alignment process. Imputed genomes are derived from genotype data, where we first construct a haplotype mosaic and then assemble an imputed genome using segments of DNA sequence from known DNA contributors.  

 

CC Founders

The CC founder strain genomes are derived from variant data and BAM files provided by the Welcome Trust Sanger Institute, and described by Keane et al. Statistics on the number of variants relative to the reference sequence are also provided.

Last update: 2012-11-08

Strain	Pseudogenome Statistics	Type	Downloads
A/J	Chromosome Length SNPs Insertions Deletions chr1 197170268 354966 92835 117999 chr2 181724043 295374 78553 102597 chr3 159577879 325244 76314 98218 chr4 155606750 260410 68355 91725 chr5 152517824 173242 52885 72320 chr6 149499604 214553 53348 70781 chr7 152504670 203165 55855 75738 chr8 131723843 285910 66844 81872 chr9 124055333 194826 56435 77274 chr10 129981208 138172 37159 49206 chr11 121818913 285286 74653 99596 chr12 121239871 239022 59351 77010 chr13 120265296 243030 60411 79427 chr14 125184858 233179 52080 62086 chr15 103481959 133214 37271 50286 chr16 98310184 113213 30402 39368 chr17 95256190 172877 46412 62873 chr18 90759912 121848 34847 46966 chr19 61332703 105499 29155 38882 chrX 166640640 105294 25440 35096 chrY 15902555 208 0 0 chrM 16299 0 0 0	sequenced	FASTA (734 MB) MOD (23 MB)
C57BL/6J	Chromosome Length SNPs Insertions Deletions chr1 197195432 0 0 0 chr2 181748087 0 0 0 chr3 159599783 0 0 0 chr4 155630120 0 0 0 chr5 152537259 0 0 0 chr6 149517037 0 0 0 chr7 152524553 0 0 0 chr8 131738871 0 0 0 chr9 124076172 0 0 0 chr10 129993255 0 0 0 chr11 121843856 0 0 0 chr12 121257530 0 0 0 chr13 120284312 0 0 0 chr14 125194864 0 0 0 chr15 103494974 0 0 0 chr16 98319150 0 0 0 chr17 95272651 0 0 0 chr18 90772031 0 0 0 chr19 61342430 0 0 0 chrX 166650296 0 0 0 chrY 15902555 0 0 0 chrM 16299 0 0 0	sequenced	FASTA (734 MB) MOD (<1 MB)
129S1/SvImJ	Chromosome Length SNPs Insertions Deletions chr1 197166043 371844 101487 130876 chr2 181722877 264696 80309 105519 chr3 159575636 259662 70163 94310 chr4 155601790 331152 88162 116492 chr5 152512035 216145 67907 93131 chr6 149494674 246601 64158 86521 chr7 152497654 267026 72107 99006 chr8 131716028 367663 91151 113994 chr9 124049394 233927 68944 95722 chr10 129981860 93531 29123 40518 chr11 121824600 166865 54506 73762 chr12 121241416 221788 58085 74199 chr13 120268361 175549 49972 65923 chr14 125166430 343586 76558 104992 chr15 103473502 255279 61791 83263 chr16 98307524 130852 36982 48608 chr17 95252763 195984 55542 75430 chr18 90754202 188490 53502 71331 chr19 61332420 102336 29791 39801 chrX 166645284 25028 12628 17640 chrY 15902555 277 0 0 chrM 16299 1 0 0	sequenced	FASTA (734 MB) MOD (25 MB)
NOD/ShiLtJ	Chromosome Length SNPs Insertions Deletions chr1 197174762 361975 88614 109284 chr2 181728042 339842 83554 103599 chr3 159584693 258158 62084 77174 chr4 155616353 231375 60130 73897 chr5 152517828 243520 60859 80290 chr6 149499122 311913 67847 85762 chr7 152509338 259031 59289 74504 chr8 131727515 292870 64740 76096 chr9 124058321 214909 53945 71796 chr10 129983041 145051 38624 48838 chr11 121827815 236877 60455 76496 chr12 121246080 213833 51051 62501 chr13 120269234 248570 54490 69568 chr14 125182743 297532 61206 73327 chr15 103484568 130201 33213 43619 chr16 98312663 97865 25174 31661 chr17 95258529 200837 47958 62080 chr18 90762803 113432 30221 39449 chr19 61336132 95128 25032 31330 chrX 166645752 30611 14037 18581 chrY 15902555 89 0 0 chrM 16299 0 0 0	sequenced	FASTA (734 MB) MOD (23 MB)
NZO/HlLtJ	Chromosome Length SNPs Insertions Deletions chr1 197175383 369662 88466 108515 chr2 181730447 299296 70821 88461 chr3 159583155 258222 61538 78166 chr4 155617734 197551 50674 63060 chr5 152519398 229999 56428 74289 chr6 149499852 306359 63144 80329 chr7 152506597 257057 58346 76302 chr8 131725371 307742 68043 81543 chr9 124054299 292135 66890 88763 chr10 129985144 110103 28276 36387 chr11 121822481 311649 71809 93184 chr12 121246163 233213 51916 63283 chr13 120266958 293927 60907 78261 chr14 125182129 290342 61324 74059 chr15 103485090 125217 30695 40579 chr16 98311998 116852 28697 35849 chr17 95261145 170446 41976 53482 chr18 90762020 136678 32743 42754 chr19 61334932 135897 30767 38265 chrX 166644079 50025 19673 25890 chrY 15902555 153 0 0 chrM 16299 54 0 0	sequenced	FASTA (734 MB) MOD (24 MB)
CAST/EiJ	Chromosome Length SNPs Insertions Deletions chr1 197149404 1399062 320272 366300 chr2 181706609 1127897 286896 328374 chr3 159564173 1128507 246296 281906 chr4 155594720 1067742 256861 292261 chr5 152495389 1078000 265154 307024 chr6 149482240 1065900 244836 279633 chr7 152488544 961145 227289 263298 chr8 131709590 954286 228262 257543 chr9 124042219 846852 212276 246229 chr10 129956235 991846 231461 268481 chr11 121807846 872829 227690 263700 chr12 121232158 816152 192841 218213 chr13 120253643 856382 198974 229643 chr14 125170107 832410 189207 213964 chr15 103468076 719344 168774 195672 chr16 98293627 713261 159872 185395 chr17 95248075 617935 150327 174903 chr18 90745931 691297 158390 184490 chr19 61325101 430739 106088 123417 chrX 166630853 502140 135010 154453 chrY 15902555 424 0 0 chrM 16299 214 0 0	sequenced	FASTA (734 MB) MOD (92 MB)
PWK/PhJ	Chromosome Length SNPs Insertions Deletions chr1 197111253 1281551 250063 334242 chr2 181653205 1229246 254388 349270 chr3 159526373 1095545 206541 279951 chr4 155556678 1067491 212538 285980 chr5 152452161 1114007 229905 315003 chr6 149446229 1018741 197711 268519 chr7 152461190 876376 173790 237153 chr8 131676074 824606 170977 233774 chr9 124007201 862426 177588 246559 chr10 129926424 984241 197868 264699 chr11 121772145 852355 187853 259564 chr12 121201461 773400 155975 212044 chr13 120230235 763230 152607 206684 chr14 125154554 584147 115554 155864 chr15 103443912 717038 139381 190443 chr16 98269094 723492 140848 190904 chr17 95226462 623210 127015 173204 chr18 90723053 697588 137067 186045 chr19 61307925 457719 96360 130865 chrX 166589221 656027 133407 194482 chrY 15902555 278 0 0 chrM 16299 221 0 0	sequenced	FASTA (734 MB) MOD (89 MB)
WSB/EiJ	Chromosome Length SNPs Insertions Deletions chr1 197166022 481174 123929 153339 chr2 181714387 404750 110186 143886 chr3 159573192 385429 94386 120977 chr4 155603393 375738 98706 125433 chr5 152507497 331040 91585 121347 chr6 149489362 397386 97210 124885 chr7 152500690 302859 79148 103011 chr8 131713668 432878 104546 129749 chr9 124051627 293254 78888 103433 chr10 129969910 310407 82771 106116 chr11 121818670 291772 81922 107108 chr12 121235953 321652 79623 101200 chr13 120262142 280138 73156 95326 chr14 125177604 348372 81398 98658 chr15 103476888 231171 60966 79052 chr16 98304102 209945 55389 70437 chr17 95254657 230767 59848 77842 chr18 90757761 171693 47109 61379 chr19 61331443 144490 38805 49792 chrX 166636948 100658 40143 53491 chrY 15902555 298 0 0 chrM 16299 4 0 0	sequenced	FASTA (734 MB) MOD (34 MB)
MD5 checksums

 

CC Strains

Last update:  2012-11-15

Strain	Pseudogenome Statistics	Type	Downloads
OR867	Chromosome Length SNPs Insertions Deletions chr1 197139045 868245 177332 233719 chr2 181717251 433929 99146 129982 chr3 159569681 394383 88641 118743 chr4 155613288 252086 65132 81964 chr5 152519701 234281 58977 76535 chr6 149494927 562209 111902 134012 chr7 152506685 245823 59173 77041 chr8 131713572 468133 104444 129743 chr9 124048514 297391 71567 99225 chr10 129965725 373981 82967 110497 chr11 121822227 454276 89126 110755 chr12 121242779 204128 51449 66200 chr13 120267786 250316 58627 75153 chr14 125178071 261660 57407 74200 chr15 103487932 98406 23679 30721 chr16 98311362 106812 28589 36377 chr17 95226462 623210 127015 173204 chr18 90735715 526963 99840 136156 chr19 61333106 117556 31223 40547 chrX 166649102 14624 3306 4500 chrY 15902555 0 0 0 chrM 16299 0 0 0	imputed	FASTA (734 MB) MOD (36 MB)
OR1237	Chromosome Length SNPs Insertions Deletions chr1 197169693 574599 124938 150677 chr2 181725475 284026 78511 101123 chr3 159587262 204965 45331 57852 chr4 155611609 439358 107883 126394 chr5 152499643 700843 141764 179380 chr6 149501688 230103 51974 67323 chr7 152496658 625005 137888 165783 chr8 131724040 293297 67658 82489 chr9 124056877 229778 56843 76138 chr10 129974947 253269 65436 83744 chr11 121818067 382021 97353 123142 chr12 121245046 325623 73842 86326 chr13 120269793 235751 51229 65748 chr14 125170911 390772 90366 114319 chr15 103486502 139694 21732 30204 chr16 98310518 116533 29793 38425 chr17 95254139 216116 55479 73991 chr18 90758916 133944 37755 50870 chr19 61338590 78741 13444 17284 chrX 166632294 225476 63556 81558 chrY 15902555 0 0 0 chrM 16299 0 0 0	imputed	FASTA (734 MB) MOD (32 MB)
OR1515	Chromosome Length SNPs Insertions Deletions chr1 197169097 739992 155615 181950 chr2 181723728 257543 74338 98697 chr3 159582754 195223 52856 69885 chr4 155593058 518930 115216 152278 chr5 152511478 249239 70554 96335 chr6 149494534 302891 73101 95604 chr7 152509200 262193 62729 78082 chr8 131721846 382903 85027 102052 chr9 124044072 516072 92898 124998 chr10 129982012 380352 59671 70914 chr11 121818167 401906 113163 138852 chr12 121237243 469871 111075 131362 chr13 120267953 366851 67174 83533 chr14 125180656 310022 72131 86339 chr15 103445371 704129 135543 185146 chr16 98308767 125895 34472 44855 chr17 95262008 202827 31674 42317 chr18 90766849 46628 12660 17842 chr19 61338941 65143 16335 19824 chrX 166647708 18818 7884 10472 chrY 15902555 0 0 0 chrM 16299 0 0 0	imputed	FASTA (734 MB) MOD (34 MB)
OR3154	Chromosome Length SNPs Insertions Deletions chr1 197172613 881321 130934 153753 chr2 181732945 272892 68820 83962 chr3 159582983 260832 61160 77960 chr4 155607286 481113 106857 129691 chr5 152518536 166132 50680 69403 chr6 149494154 529586 120575 143458 chr7 152497879 508806 88634 115308 chr8 131735695 269071 28280 31456 chr9 124069620 69870 16229 22781 chr10 129977593 321391 75852 91514 chr11 121824867 342984 80174 99163 chr12 121240224 262443 63930 81236 chr13 120274136 159017 33311 43487 chr14 125180702 321976 66451 80613 chr15 103462267 489432 99103 131810 chr16 98310718 97720 27383 35815 chr17 95256738 216622 56361 72274 chr18 90751563 369222 57511 77979 chr19 61331012 133871 36298 47716 chrX 166646476 25513 12201 16021 chrY 15902555 0 0 0 chrM 16299 0 0 0	imputed	FASTA (734 MB) MOD (32 MB)
OR3252	Chromosome Length SNPs Insertions Deletions chr1 197170137 411898 100763 126058 chr2 181724256 260329 74404 98235 chr3 159584673 234966 52185 67295 chr4 155595681 488395 103381 137820 chr5 152522630 246083 57918 72547 chr6 149495358 276585 65711 87390 chr7 152506024 202463 55580 74109 chr8 131717198 558103 126022 147695 chr9 124068143 87479 20605 28634 chr10 129980579 148689 38995 51671 chr11 121826318 227950 63558 81096 chr12 121217041 673900 120017 160506 chr13 120278300 56014 16724 22736 chr14 125173052 263519 60799 82611 chr15 103479983 173714 45560 60551 chr16 98298347 361634 69880 90683 chr17 95257113 362572 52979 68517 chr18 90762761 108587 26953 36223 chr19 61342089 207 466 807 chrX 166631813 184090 41525 60008 chrY 15902555 0 0 0 chrM 16299 0 0 0	imputed	FASTA (734 MB) MOD (28 MB)
OR559	Chromosome Length SNPs Insertions Deletions chr1 197172421 636155 131404 154415 chr2 181729383 486935 62391 81095 chr3 159564599 833483 182963 218147 chr4 155602301 570116 136673 164492 chr5 152516359 211593 61915 82815 chr6 149498924 331884 72552 90665 chr7 152498378 266250 71839 98014 chr8 131708723 803755 183025 213173 chr9 124057910 204755 50234 68496 chr10 129968714 666180 149183 173724 chr11 121811176 563763 145583 178263 chr12 121239871 239022 59351 77010 chr13 120270535 210964 42413 56190 chr14 125168494 319645 70593 96963 chr15 103477064 229879 60208 78118 chr16 98312819 115035 24826 31157 chr17 95255127 190167 48709 66233 chr18 90754583 313666 76411 93859 chr19 61335231 90173 24001 31200 chrX 166648091 14648 5532 7737 chrY 15902555 0 0 0 chrM 16299 0 0 0	imputed	FASTA (734 MB) MOD (38 MB)
IL16211	Chromosome Length SNPs Insertions Deletions chr1 197165980 428122 112317 141769 chr2 181730220 273577 66576 84443 chr3 159585357 249361 59302 73728 chr4 155617659 164523 44524 56985 chr5 152524075 263714 60974 74158 chr6 149494108 312577 74924 97853 chr7 152503091 267703 68755 90217 chr8 131736567 21096 5829 8133 chr9 124029253 797494 180929 227848 chr10 129978013 222318 51255 66497 chr11 121822140 320328 73756 95472 chr12 121240130 271185 61071 78471 chr13 120266909 229855 54256 71659 chr14 125171496 462047 99765 123133 chr15 103482243 143725 36746 49477 chr16 98310904 113808 29213 37459 chr17 95260712 159769 41011 52950 chr18 90757003 145540 42098 57126 chr19 61332703 105499 29155 38882 chrX 166633484 177523 33938 50750 chrY 15902555 0 0 0 chrM 16299 0 0 0	imputed	FASTA (734 MB) MOD (28 MB)
IL16188	Chromosome Length SNPs Insertions Deletions chr1 197168202 441424 109006 136236 chr2 181722442 327373 88198 113843 chr3 159582750 417109 85879 102912 chr4 155613112 228373 57825 74833 chr5 152496758 524537 118386 158887 chr6 149495733 264089 64627 85931 chr7 152511854 188291 37402 50101 chr8 131722243 389082 72928 89556 chr9 124053547 325942 75769 98394 chr10 129976780 192816 51759 68234 chr11 121821513 263395 69456 91799 chr12 121234108 441910 107405 130827 chr13 120264364 229454 60707 80655 chr14 125176489 525319 110164 128539 chr15 103485287 99350 24772 34459 chr16 98313494 60037 16848 22504 chr17 95256570 200152 55185 71266 chr18 90753884 266316 56239 74386 chr19 61318102 294392 66765 91093 chrX 166640156 80107 31919 42059 chrY 15902555 0 0 0 chrM 16299 0 0 0	imputed	FASTA (734 MB) MOD (31 MB)
OR477	Chromosome Length SNPs Insertions Deletions chr1 197153097 836226 143853 186188 chr2 181728410 421246 70199 89876 chr3 159569524 759124 153440 183699 chr4 155610141 265742 66662 86641 chr5 152524565 155460 35181 47875 chr6 149486086 451467 103890 134841 chr7 152509527 224435 49477 64503 chr8 131735825 23564 6764 9810 chr9 124054494 299898 68549 90227 chr10 129980571 147540 39222 51906 chr11 121825998 256587 63127 80985 chr12 121245201 188533 41892 54221 chr13 120272853 256554 41885 53344 chr14 125175856 241896 57458 76466 chr15 103473249 297125 63206 84931 chr16 98314448 65670 17058 21760 chr17 95256104 225230 55750 72297 chr18 90757761 171693 47109 61379 chr19 61340603 21758 5569 7396 chrX 166645684 22305 11829 16441 chrY 15902555 0 0 0 chrM 16299 0 0 0	imputed	FASTA (734 MB) MOD (28 MB)
OR5489	Chromosome Length SNPs Insertions Deletions chr1 197170746 416150 106925 131611 chr2 181731206 265284 65420 82301 chr3 159557337 703066 141339 183785 chr4 155600488 470084 89907 119539 chr5 152505493 366931 97344 129110 chr6 149502210 306652 53531 68358 chr7 152504072 312456 78923 99404 chr8 131727462 308217 59505 70914 chr9 124051979 264335 67425 91618 chr10 129942395 795979 170828 221688 chr11 121819984 296886 73308 97180 chr12 121214825 644940 122046 164751 chr13 120267668 269811 59880 76524 chr14 125175821 234030 55616 74659 chr15 103470669 289225 63912 88217 chr16 98311783 236116 44637 52004 chr17 95262318 155611 30867 41200 chr18 90756716 176165 49987 65302 chr19 61338658 60392 13595 17367 chrX 166640640 105294 25440 35096 chrY 15902555 0 0 0 chrM 16299 0 0 0	imputed	FASTA (734 MB) MOD (35 MB)
AU8041	Chromosome Length SNPs Insertions Deletions chr1 197170825 391569 99138 123745 chr2 181668736 1114526 229479 308830 chr3 159593974 121238 27537 33346 chr4 155615297 220756 55963 70786 chr5 152517029 242502 63390 83620 chr6 149498316 267889 67502 86223 chr7 152508787 164774 42698 58464 chr8 131727657 263722 59353 70567 chr9 124036354 603518 147970 187788 chr10 129952569 836428 170972 211658 chr11 121816323 696333 139158 166691 chr12 121238736 254735 64674 83468 chr13 120275058 155553 31011 40265 chr14 125171252 405734 87905 111517 chr15 103485595 112430 29190 38569 chr16 98292299 571315 130626 157477 chr17 95272209 519 782 1224 chr18 90754407 256136 64084 81708 chr19 61336834 101888 16633 22229 chrX 166647003 18150 7123 10416 chrY 15902555 0 0 0 chrM 16299 0 0 0	imputed	FASTA (734 MB) MOD (36 MB)
AU8043	Chromosome Length SNPs Insertions Deletions chr1 197154356 605714 152822 193898 chr2 181746649 14317 3677 5115 chr3 159577775 609896 136417 158425 chr4 155604444 343769 86339 112015 chr5 152516355 240458 61439 82343 chr6 149495717 343056 70973 92293 chr7 152478721 651387 128635 174467 chr8 131731551 94512 17215 24535 chr9 124053526 211584 59637 82283 chr10 129974142 274008 66856 85969 chr11 121818422 711359 154817 180251 chr12 121247933 168067 38629 48226 chr13 120267636 236819 58215 74891 chr14 125183427 308145 51370 62807 chr15 103474322 261502 59964 80616 chr16 98290734 361866 82957 111373 chr17 95246734 333101 78729 104646 chr18 90756306 198185 52830 68555 chr19 61335380 119580 29969 37019 chrX 166640213 151039 24865 34948 chrY 15902555 0 0 0 chrM 16299 0 0 0	imputed	FASTA (734 MB) MOD (33 MB)
MD5 checksums

Sanger Strains

We also present pseudogenomes of other mouse strains from the Mouse Genomes Project in Wellcome Trust Sanger Institute.

The variants are derived from the SNPs and indels data sets in ftp://ftp-mouse.sanger.ac.uk/REL-1111-SNPs/ . 

Last update: 2012-11-19

Strain	Pseudogenome Statistics	Type	Downloads
129P2/OlaHsd	Chromosome Length SNPs Insertions Deletions chr1 197151672 502257 143323 187083 chr2 181712426 346084 110265 145926 chr3 159564314 341090 96874 132343 chr4 155586487 456054 116246 159879 chr5 152504262 290291 94466 127463 chr6 149483702 330541 87907 121242 chr7 152483127 516042 122743 164169 chr8 131703741 479406 119905 155035 chr9 124041347 305733 93183 128008 chr10 129973269 166958 51274 71260 chr11 121820073 226233 75061 98844 chr12 121233238 313714 76906 101198 chr13 120259936 252377 71067 95443 chr14 125158486 444454 102549 138927 chr15 103467137 326464 83416 111253 chr16 98298974 173690 50743 70919 chr17 95245593 268712 75609 102667 chr18 90749800 245310 74340 96571 chr19 61328153 135666 39781 54058 chrX 166642330 41096 20201 28167 chrY 15902555 0 0 0 chrM 16299 0 0 0	sequenced	FASTA (734 MB) MOD (33 MB)
129S5SvEvBrd	Chromosome Length SNPs Insertions Deletions chr1 197171552 491656 93086 116966 chr2 181726928 340537 72732 93891 chr3 159579454 335935 62983 83312 chr4 155605756 449440 79993 104357 chr5 152516001 285644 61656 82914 chr6 149498202 324195 58825 77660 chr7 152499850 352713 66406 91109 chr8 131720802 469877 83904 101973 chr9 124053428 301327 63188 85932 chr10 129983646 130654 26398 36007 chr11 121827443 222149 48814 65227 chr12 121243779 306231 53213 66964 chr13 120269955 232147 44590 58947 chr14 125172877 435807 71125 93112 chr15 103477862 320244 56238 73350 chr16 98310153 167060 33336 42333 chr17 95255283 262961 49866 67234 chr18 90756863 241067 48383 63551 chr19 61333862 133331 26918 35486 chrX 166646360 41022 11157 15093 chrY 15902555 0 0 0 chrM 16299 0 0 0	sequenced	FASTA (734 MB) MOD (29 MB)
AKR/J	Chromosome Length SNPs Insertions Deletions chr1 197152269 570065 155396 198559 chr2 181715897 361439 105897 138087 chr3 159571985 346177 94606 122404 chr4 155599590 365577 94320 124850 chr5 152506887 281389 88927 119299 chr6 149489461 357665 86151 113727 chr7 152499226 275591 78801 104128 chr8 131711225 414605 103445 131091 chr9 124043699 332499 90264 122737 chr10 129976273 173815 51813 68795 chr11 121810951 333669 96835 129740 chr12 121238407 294752 71054 90177 chr13 120257291 351447 88751 115772 chr14 125174895 347016 80823 100792 chr15 103484024 129809 41732 52682 chr16 98308108 121169 37128 48170 chr17 95251882 232322 65641 86410 chr18 90752595 195000 59131 78567 chr19 61328552 133680 40681 54559 chrX 166642495 46147 24184 31985 chrY 15902555 0 0 0 chrM 16299 0 0 0	sequenced	FASTA (734 MB) MOD (31 MB)
BALB/cJ	Chromosome Length SNPs Insertions Deletions chr1 197171622 356640 87390 111200 chr2 181726402 272018 72648 94333 chr3 159577153 348938 82570 105200 chr4 155602598 389040 92243 119765 chr5 152510460 288431 81129 107928 chr6 149496901 282765 66037 86173 chr7 152501021 281138 71568 95100 chr8 131715990 445136 100467 123348 chr9 124054054 234380 64481 86599 chr10 129977605 193512 48528 64178 chr11 121823351 276385 73792 94297 chr12 121240330 290450 64065 81265 chr13 120267992 251066 62750 79070 chr14 125181095 310933 65418 79187 chr15 103485287 125926 32875 42562 chr16 98308246 132277 34790 45694 chr17 95256387 214253 52329 68593 chr18 90758257 175475 48486 62260 chr19 61330236 146950 38016 50210 chrX 166636549 151142 37500 51247 chrY 15902555 0 0 0 chrM 16299 0 0 0	sequenced	FASTA (734 MB) MOD (27 MB)
C3H/HeJ	Chromosome Length SNPs Insertions Deletions chr1 197162976 469451 126534 158990 chr2 181714610 433922 114005 147482 chr3 159571183 410954 102003 130603 chr4 155604337 342650 90776 116559 chr5 152511788 267602 81975 107446 chr6 149492086 332344 81329 106280 chr7 152499661 350071 87381 112273 chr8 131715815 375195 92605 115661 chr9 124049422 257157 77608 104358 chr10 129976750 178576 50392 66897 chr11 121817193 340807 91675 118338 chr12 121237662 322130 78860 98728 chr13 120265423 256382 67326 86215 chr14 125176263 362362 77434 96035 chr15 103480301 188625 53399 68072 chr16 98303384 176850 45207 60973 chr17 95252492 245274 64706 84865 chr18 90757558 160495 50221 64694 chr19 61330042 146885 41974 54362 chrX 166637719 140018 35022 47599 chrY 15902555 0 0 0 chrM 16299 0 0 0	sequenced	FASTA (734 MB) MOD (31 MB)
C57BL/6NJ	Chromosome Length SNPs Insertions Deletions chr1 197194415 7464 1619 2636 chr2 181747503 5371 1547 2131 chr3 159599110 5484 1235 1908 chr4 155629591 6383 1306 1835 chr5 152536263 6343 1143 2139 chr6 149516225 4772 1017 1829 chr7 152523757 4989 1061 1857 chr8 131738082 4663 1160 1949 chr9 124075587 4529 1094 1679 chr10 129992483 5090 1045 1817 chr11 121843362 4929 1031 1525 chr12 121257097 3994 894 1327 chr13 120283829 4386 988 1471 chr14 125194543 3706 940 1261 chr15 103494364 3183 726 1336 chr16 98318741 3688 847 1256 chr17 95272209 4458 782 1224 chr18 90771632 3069 725 1124 chr19 61342089 2063 466 807 chrX 166649914 5650 991 1373 chrY 15902555 0 0 0 chrM 16299 0 0 0	sequenced	FASTA (734 MB) MOD (<1 MB)
CBA/J	Chromosome Length SNPs Insertions Deletions chr1 197161146 438005 109129 143415 chr2 181718360 361696 91088 120815 chr3 159568515 422378 95180 126448 chr4 155603309 338454 80943 107754 chr5 152511180 259272 70512 96591 chr6 149490947 329150 72554 98644 chr7 152497482 349833 78981 106052 chr8 131714581 412043 91290 115580 chr9 124046229 330756 81042 110985 chr10 129979154 166250 43421 57522 chr11 121817535 334327 85048 111369 chr12 121236457 333123 74272 95345 chr13 120263781 254265 60568 81099 chr14 125172616 422365 85118 107366 chr15 103479085 183669 46612 62501 chr16 98298711 257929 57841 78280 chr17 95250932 243203 57218 78937 chr18 90755048 161666 43880 60863 chr19 61328594 163174 40813 54649 chrX 166638169 137026 30361 42488 chrY 15902555 0 0 0 chrM 16299 0 0 0	sequenced	FASTA (734 MB) MOD (31 MB)
DBA/2J	Chromosome Length SNPs Insertions Deletions chr1 197159703 578926 114497 150226 chr2 181716658 442685 91729 123158 chr3 159574598 373067 73598 98783 chr4 155604366 375583 73686 99440 chr5 152511795 280335 62185 87649 chr6 149494754 305308 57539 79822 chr7 152492808 431130 77496 109241 chr8 131719901 382643 72208 91178 chr9 124052396 257811 55409 79185 chr10 129978161 200656 40697 55791 chr11 121818339 328388 66951 92468 chr12 121243679 287861 51120 64971 chr13 120268617 216365 42997 58692 chr14 125174842 430040 74138 94160 chr15 103479504 175864 37371 52841 chr16 98307261 159547 34423 46312 chr17 95253236 260174 49744 69159 chr18 90760815 127993 28527 39743 chr19 61329325 167643 35080 48185 chrX 166645832 39706 12646 17110 chrY 15902555 0 0 0 chrM 16299 0 0 0	sequenced	FASTA (734 MB) MOD (30 MB)
FVB/NJ	Chromosome Length SNPs Insertions Deletions chr1 197156824 385486 119871 158479 chr2 181710755 302932 99259 136591 chr3 159570409 281472 83690 113064 chr4 155603156 239030 78458 105422 chr5 152511164 209952 74572 100667 chr6 149487981 289096 88082 117138 chr7 152500471 206438 63978 88060 chr8 131712790 303084 87057 113138 chr9 124042695 259758 85450 118927 chr10 129973824 154387 48632 68063 chr11 121818785 196324 65582 90653 chr12 121233455 271363 76063 100138 chr13 120261955 216212 65173 87530 chr14 125171604 276887 75225 98485 chr15 103476629 138656 46445 64790 chr16 98302517 125857 41012 57645 chr17 95253246 167155 53174 72579 chr18 90756049 123283 42034 58016 chr19 61326491 133499 42471 58410 chrX 166642346 32078 20147 28097 chrY 15902555 0 0 0 chrM 16299 0 0 0	sequenced	FASTA (734 MB) MOD (25 MB)
LP/J	Chromosome Length SNPs Insertions Deletions chr1 197166347 483279 111695 140780 chr2 181725072 330053 87793 110808 chr3 159575222 336805 80293 104854 chr4 155600793 454107 96994 126321 chr5 152512528 286724 77754 102485 chr6 149490408 377377 82388 109017 chr7 152498435 356428 80280 106398 chr8 131715720 457705 101391 124542 chr9 124045952 343941 86453 116673 chr10 129976845 187501 49613 66023 chr11 121821592 291021 77644 99908 chr12 121244743 248119 56159 68946 chr13 120260433 340047 75648 99527 chr14 125163863 529711 96203 127204 chr15 103475136 314967 69244 89082 chr16 98307541 152700 39226 50835 chr17 95253703 240782 56431 75379 chr18 90754439 242650 60982 78574 chr19 61332809 134066 33577 43198 chrX 166645010 39503 15038 20324 chrY 15902555 0 0 0 chrM 16299 0 0 0	sequenced	FASTA (734 MB) MOD (32 MB)
SPRET/EiJ	Chromosome Length SNPs Insertions Deletions chr1 197091310 3304812 479548 583670 chr2 181641054 2907299 455538 562571 chr3 159517832 2704918 382492 464443 chr4 155545098 2501077 378374 463396 chr5 152439188 2510334 385923 483994 chr6 149434791 2454316 359775 442021 chr7 152448257 2129428 322980 399276 chr8 131660386 2178036 327601 406086 chr9 123996159 2038814 320934 400947 chr10 129917389 2256219 339938 415804 chr11 121755809 2009676 330909 418956 chr12 121195256 1892926 282512 344786 chr13 120214922 1946969 290456 359846 chr14 125134431 1992735 287896 348329 chr15 103436340 1783223 264849 323483 chr16 98262945 1682638 246914 303119 chr17 95214081 1530847 229543 288113 chr18 90715834 1521704 227351 283548 chr19 61304404 1003325 160214 198240 chrX 166591727 1795575 264129 322698 chrY 15902555 0 0 0 chrM 16299 0 0 0	sequenced	FASTA (734 MB) MOD (193 MB)
MD5 checksums

 

Pseudogenome Tools

We provide a suite of tools that simplify the incorporation of our pseudogenomes into standard analysis and hiseq pipelines. 

[Lapels]

Lapels is used to remap pseudogenome alignments, in the form of a BAM file, back to the reference sequence. This entails the removal of all indels (via the cigar string modifications, the underlying sequence is unaltered) and adjustments to the fragment and its mate's starting positions. Lapels also annotates the number and types (SNPs, insertions, and deletions) of sequence variants seen in each read.

The input includes the BAM file of psedogenome alignment and the MOD file associated with the FASTA sequences used in the alignment. (Please bundle MOD and FASTA while downloading.)

The output is a BAM file with corrected reads positions, cigar strings, and annotated tags. It has been tested to be compatible with downstream tools, such as IGV (using the reference genome) and Cufflinks (using any referenced based transcript library).

The code for Lapels is written in Python and can be downloaded as a tarball from here. It requires the pysam library and the argparse library.

The code and documentation are hosted in http://code.google.com/p/lapels/.

Please report bugs or give suggestions in http://code.google.com/p/lapels/issues/list .

 

[Suspenders]

Suspenders merges the results of multiple alignments (BAM files) applied to the same set of reads. It is used when working with F1 and RIX crosses, where we suggest performing separate alignments to each parental genome. Suspenders then effectively merges and annotates these separate BAM files into a single consensus BAM file.

When reads map to the same genomic location in both alignments, only one read is output. Where there are differences in either mapping positions or multiplicity of reads, Suspenders determines the most likely alignment and source genome for the read, which is sent to the output BAM file. When there is no significant difference in the alignments all multiple mappings are output.

Suspenders is written in Python. It requires the pysam library and the argparse libraries.

The code for Suspenders is available in http://code.google.com/p/suspenders/.

 

Publications

S. Huang, C.-Y. Kao, L. McMillan, and W. Wang.Transforming genomes using mod files with applications. In Proceedings of the ACM Conferenceon Bioinformatics, Computational Biology and Biomedicine. ACM, 2013. [link]

J. Holt, S. Huang, L. McMillan, and W. Wang. Read annotation pipeline for high-throughput sequencing data. In Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM, 2013. [link]