MGI_4.01 - dbSNP Load Detail

SNP Data in MGI

Provider
Version

NCBI dbSNP dbSNP Home
Build 126

Description

MGI loads mouse SNP data from dbSNP in conjunction with new dbSNP build releases. MGI loads mouse Reference SNPs (rs) and their corresponding submitted SNP assays (ss), where at least one ss assay of a Reference SNP has strains defined for the alleles submitted.
MGI does not load the following:
- SNPs (rs and ss) that have no submitted assays with defined strain/allele relationships.
- Submitted SNP (ss) strain alleles where the value of the strain allele is "N" (N= Allele determination failed for that strain).
- SNPs (rs) where all submitted SNP strain alleles have value "N".
- SNPs (rs and ss) that map to more than one chromosome in the C57BL/6J genome.
- SNPs (rs and ss) that map to more than two locations on the same chromosome in the C57BL/6J genome.
- SNPs (rs and ss) that are unmapped in the C57BL/6J genome.

dbSNP Build Statistics | dbSNP Reference SNPs not loaded (100+ Mb)

Statistics

All values are for data loaded into MGI.
Note: Some values for number of SNPs in MGI may differ from Provider values. See Description above for statement on SNP loads.

Total Assays (ss) 6,938,078

Total RefSNPs (rs) 6,348,628

Assays per RefSNP (ss/rs) 1.0928

Total Strains with SNP data 87

Assays (ss) per Submitter

PERLEGEN 3,954,108

ABI 2,475,864

WI 338,758

ROCHEBIO 77,215

CRAMUS 68,508

TWGNF 20,407

WIMOUSESNPS 1,992

KOKORO_BIOLOGY_GROUP 818

ERO 368

MITCCR 38

TIZUMI 1

NCBI-GENBANK-VAR 1

Total Assays 6,938,078

RefSNPs (rs) per Strain by Chromosome

Strain Chr 1 Chr 2 Chr 3 Chr 4 Chr 5 Chr 6 Chr 7 Chr 8 Chr 9 Chr 10 Chr 11 Chr 12 Chr 13 Chr 14 Chr 15 Chr 16 Chr 17 Chr 18 Chr 19 Chr X Chr Y All Chromosomes Strain

All Strains 599,292 683,594 357,920 590,844 373,128 366,771 310,574 265,696 263,334 157,793 378,812 182,123 233,828 300,336 247,492 140,362 155,698 287,698 223,532 229,645 155 6,348,627 All Strains

A/J 533,809 600,420 312,107 513,833 333,511 321,169 271,999 229,856 231,069 130,771 324,159 155,136 204,837 264,465 216,989 119,647 132,531 257,125 200,521 202,941 134 5,557,029 A/J

DBA/2J 512,254 553,378 295,142 517,005 313,991 308,739 253,267 210,794 217,213 123,485 316,776 143,957 193,694 248,259 205,883 111,905 126,143 251,130 187,594 193,029 125 5,283,763 DBA/2J

129S1/SvImJ 408,338 512,192 210,811 450,917 243,245 252,652 163,078 146,648 161,616 89,396 264,660 87,297 142,327 177,574 146,814 74,818 76,300 213,802 170,142 168,938 46 4,161,611 129S1/SvImJ

BALB/cByJ 368,508 485,487 159,762 410,529 215,369 228,403 129,090 110,931 130,745 66,802 229,883 53,275 115,103 142,474 125,596 57,718 46,506 190,573 161,238 156,115 10 3,584,117 BALB/cByJ

AKR/J 349,335 471,980 161,241 406,197 214,339 221,720 127,931 110,443 133,871 70,318 225,236 50,929 110,512 143,964 127,728 59,364 49,688 189,184 156,199 160,810 5 3,540,994 AKR/J

C3H/HeJ 358,818 464,337 157,288 414,863 212,891 224,537 127,788 108,351 129,841 68,076 235,870 50,499 106,925 141,414 126,559 57,738 48,674 182,098 155,665 159,415 9 3,531,656 C3H/HeJ

NZW/LacJ 352,846 470,246 159,203 422,142 208,251 219,005 117,943 106,624 127,999 68,093 232,034 53,296 109,273 133,478 121,353 54,589 46,873 186,706 152,519 158,394 4 3,500,871 NZW/LacJ

NOD/LtJ 351,227 467,143 158,760 424,460 200,881 219,700 120,727 104,952 125,385 66,216 228,333 49,759 108,029 137,159 125,279 53,966 45,716 186,213 157,974 164,965 6 3,496,850 NOD/LtJ

FVB/NJ 354,416 476,635 156,914 421,000 202,398 217,468 120,905 106,164 123,332 63,678 228,059 50,138 109,651 137,672 118,625 51,407 41,561 187,194 155,421 161,885 5 3,484,528 FVB/NJ

KK/HlJ 349,581 450,975 159,477 410,440 203,475 218,571 118,338 105,628 129,789 68,802 228,533 51,923 107,413 138,223 125,258 55,522 47,447 182,176 156,529 163,743 6 3,471,849 KK/HlJ

WSB/EiJ 350,504 472,023 155,060 414,816 197,524 211,227 117,956 105,908 129,177 68,987 220,293 52,451 109,269 138,331 123,494 55,064 46,157 185,283 154,510 158,986 6 3,467,026 WSB/EiJ

BTBR T<+> tf/J 355,844 470,437 162,355 394,220 208,077 220,704 117,935 100,926 128,643 64,845 219,249 49,620 110,935 136,187 117,252 54,413 46,353 187,585 157,460 154,813 5 3,457,858 BTBR T<+> tf/J

CAST/EiJ 348,298 448,251 156,495 392,627 212,429 214,142 120,030 104,248 126,911 67,162 191,084 52,513 108,852 128,652 109,154 51,476 42,693 180,433 150,962 159,475 10 3,365,897 CAST/EiJ

MOLF/EiJ 335,284 457,957 148,790 403,163 183,826 217,566 117,391 106,516 123,962 65,064 213,814 43,411 100,081 127,747 120,272 52,014 42,631 180,668 146,484 146,645 5 3,333,291 MOLF/EiJ

PWD/PhJ 336,577 448,065 147,864 382,230 188,258 205,969 114,856 104,444 119,584 61,330 224,795 46,340 104,273 128,332 111,369 49,306 41,425 169,226 150,099 151,759 0 3,286,101 PWD/PhJ

C57BL/6J 224,286 185,072 178,568 159,301 147,684 128,709 164,825 141,995 121,737 78,222 133,004 115,296 108,961 147,035 113,036 79,019 100,470 87,958 57,951 60,221 62 2,533,412 C57BL/6J

129X1/SvJ 162,173 133,556 128,306 118,493 110,874 88,855 122,753 101,341 88,233 50,351 95,311 82,838 77,740 107,737 84,172 52,921 70,997 64,870 39,733 29,416 71 1,810,741 129X1/SvJ

CZECHII/EiJ 19,150 18,056 16,507 15,116 15,585 15,476 13,170 12,177 12,766 13,747 12,846 11,904 11,880 11,224 10,840 10,186 9,127 10,133 6,443 6,101 6 252,440 CZECHII/EiJ

SPRET/EiJ 8,184 4,863 2,969 2,933 12,481 4,000 7,931 3,206 3,873 2,075 6,106 1,983 1,926 2,297 2,506 3,028 3,543 3,003 2,750 2,500 9 82,166 SPRET/EiJ

NZB/BlNJ 8,044 4,446 2,454 2,664 13,183 3,869 7,749 3,067 3,063 1,597 6,200 1,633 1,427 2,254 2,075 2,866 3,228 3,093 2,066 2,252 6 77,236 NZB/BlNJ

MRL/MpJ 7,400 4,273 1,900 1,901 12,130 3,343 7,465 2,666 2,665 1,899 5,669 1,213 1,198 1,863 1,966 2,599 2,703 3,135 2,265 1,746 0 69,999 MRL/MpJ

B10.D2-Hc<0> H2<d> H2-T18<c>/oSnJ 7,162 4,119 1,786 1,910 12,348 3,138 7,130 2,078 2,972 1,591 5,492 1,361 1,099 1,582 1,995 2,496 2,727 3,172 2,017 1,824 0 67,999 B10.D2-Hc<0> H2<d> H2-T18<c>/oSnJ

BALB/cJ 6,657 4,280 1,913 1,841 11,183 3,125 7,011 2,295 2,853 1,887 5,272 1,347 1,128 1,920 1,996 2,596 2,786 3,038 1,935 2,099 0 67,162 BALB/cJ

A/HeJ 6,884 3,897 1,785 1,893 12,169 3,068 7,140 2,448 2,604 1,059 5,411 1,351 1,045 1,529 1,897 2,416 2,493 2,855 1,993 1,926 0 65,863 A/HeJ

129/Sv 4,801 4,364 2,621 2,150 5,522 3,914 7,348 2,927 3,615 2,224 2,625 1,799 1,710 2,098 2,201 2,755 3,146 833 2,223 2,288 4 61,168 129/Sv

NZW/Lac 3,760 4,101 1,753 1,537 4,930 3,051 6,903 2,666 2,606 1,183 2,652 1,369 1,044 1,538 1,840 2,486 2,841 386 2,165 1,814 0 50,625 NZW/Lac

SM/J 2,380 3,480 1,519 1,444 3,822 3,123 3,875 1,980 2,266 987 1,489 959 1,154 1,429 1,294 1,069 1,946 354 915 858 5 36,348 SM/J

LP/J 2,317 3,439 1,499 1,333 3,855 3,015 3,644 1,914 2,198 791 1,502 962 1,054 1,331 1,464 1,037 1,841 354 936 769 5 35,260 LP/J

LG/J 2,123 3,368 1,135 1,452 3,191 2,629 3,014 1,940 2,166 791 1,507 933 947 1,274 1,258 1,092 1,661 340 933 756 5 32,515 LG/J

FVB 1,329 2,368 817 650 3,124 2,373 2,654 861 1,566 266 673 447 579 708 998 655 1,367 0 538 289 0 22,262 FVB

BUB 1,222 2,350 839 557 3,087 2,360 2,646 893 1,554 255 559 490 615 672 1,028 652 1,391 0 426 298 0 21,894 BUB

PERA 1,345 2,315 849 630 2,901 2,315 2,651 838 1,589 280 625 489 567 672 936 663 1,389 0 505 305 0 21,864 PERA

MOLF 723 841 836 243 850 1,961 2,321 504 1,602 267 513 476 551 549 928 307 1,079 0 224 195 0 14,970 MOLF

DBA/1J 631 656 555 561 511 462 485 478 437 338 451 375 373 414 374 300 340 1,142 216 311 5 9,415 DBA/1J

CBA/J 678 676 580 595 550 513 517 497 448 357 585 399 394 425 389 316 372 347 225 335 6 9,204 CBA/J

SWR/J 643 675 566 611 552 501 512 515 448 368 500 392 399 440 399 322 380 347 221 343 6 9,140 SWR/J

MSM/Ms 559 614 516 540 477 430 475 474 417 326 440 356 353 387 361 291 330 1,117 208 306 5 8,982 MSM/Ms

JF1/Ms 543 611 506 536 499 443 469 456 407 334 442 364 359 394 354 284 330 1,112 204 307 6 8,960 JF1/Ms

BUB/BnJ 648 655 563 586 545 509 501 485 450 350 467 392 386 419 394 314 354 338 221 328 6 8,911 BUB/BnJ

SEA/GnJ 650 659 573 581 543 495 502 482 436 345 477 388 376 426 384 303 357 338 221 327 5 8,868 SEA/GnJ

C57BR/cdJ 643 655 573 578 547 493 497 489 444 353 471 392 372 424 378 311 361 338 220 322 5 8,866 C57BR/cdJ

RIIIS/J 646 673 562 577 539 497 487 490 439 354 470 389 375 420 386 309 360 326 221 332 5 8,857 RIIIS/J

C57BL/10J 638 657 570 587 542 485 494 485 441 353 467 400 375 417 387 308 356 340 218 324 6 8,850 C57BL/10J

SJL/J 639 663 574 570 534 484 488 486 446 342 462 383 388 426 376 302 353 338 221 327 6 8,808 SJL/J

PERA/EiJ 631 655 562 578 523 497 496 490 436 345 459 391 384 418 377 310 348 339 219 324 6 8,788 PERA/EiJ

C58/J 635 655 553 576 534 490 502 484 436 352 455 394 376 421 379 307 355 340 222 317 5 8,788 C58/J

DDK/Pas 635 666 566 577 543 493 493 481 434 346 454 382 382 418 385 311 351 318 222 313 5 8,775 DDK/Pas

C57L/J 625 647 555 567 532 501 491 485 446 354 467 391 387 421 370 295 353 335 220 329 4 8,775 C57L/J

CE/J 636 656 551 568 535 495 493 477 439 348 460 389 379 420 377 301 351 335 222 319 5 8,756 CE/J

MA/MyJ 599 657 555 553 528 488 498 480 426 354 467 380 384 422 386 315 360 339 223 325 5 8,744 MA/MyJ

C57BLKS/J 618 650 556 560 530 488 494 469 440 340 464 386 376 414 372 311 350 336 223 323 4 8,704 C57BLKS/J

PL/J 618 657 556 573 530 480 489 457 428 353 459 380 376 406 370 306 344 337 220 329 6 8,674 PL/J

ST/bJ 610 657 547 556 518 484 498 478 433 347 459 389 369 409 378 309 348 326 221 310 6 8,652 ST/bJ

I/LnJ 598 647 552 573 529 497 497 468 428 347 456 393 385 402 375 306 343 329 214 307 4 8,650 I/LnJ

NON/LtJ 605 644 554 562 504 466 478 455 426 333 447 370 360 397 367 307 335 327 210 312 6 8,465 NON/LtJ

MSM 276 727 448 138 0 299 1,471 293 1,042 246 448 308 385 323 670 377 683 0 227 0 0 8,361 MSM

ZALENDE/EiJ 587 637 532 533 504 454 476 444 408 334 440 369 352 401 353 301 345 317 219 316 6 8,328 ZALENDE/EiJ

MAI/Pas 567 599 500 527 467 439 468 452 397 319 420 359 346 380 349 284 324 300 202 290 5 7,994 MAI/Pas

PWD/Ph 565 593 494 516 468 407 460 434 402 312 419 358 357 387 334 278 325 293 191 299 5 7,897 PWD/Ph

SEG/Pas 477 516 411 449 397 354 375 363 346 251 364 308 284 333 295 242 269 266 172 250 4 6,726 SEG/Pas

AKR 147 140 105 136 121 133 126 86 89 79 161 92 110 74 81 81 48 94 43 26 0 1,972 AKR

C57BL/6 147 143 111 126 121 132 126 85 93 78 140 92 110 76 84 82 51 94 43 26 0 1,960 C57BL/6

C3H/He 148 140 109 126 119 135 123 86 89 74 146 90 108 77 83 84 51 96 43 25 0 1,952 C3H/He

A 145 142 108 127 121 134 127 85 91 76 141 90 108 77 85 82 48 94 42 22 0 1,945 A

BALB/cBy 146 140 106 125 121 131 126 85 88 74 143 91 108 76 81 79 49 95 43 25 0 1,932 BALB/cBy

129X1/Sv 145 139 103 121 120 129 123 80 88 76 143 91 108 76 83 78 46 93 43 25 0 1,910 129X1/Sv

DBA/2 146 135 107 122 118 130 124 84 86 78 135 86 109 77 80 79 49 90 43 25 0 1,903 DBA/2

SWN/Ms 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 812 0 0 0 812 SWN/Ms

NJL/Ms 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 812 0 0 0 812 NJL/Ms

KJR/Ms 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 812 0 0 0 812 KJR/Ms

HMI/Ms 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 812 0 0 0 812 HMI/Ms

CHD/Ms 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 812 0 0 0 812 CHD/Ms

BLG2/Ms 0 0 0 0 0 0 0 0 0 0