Summary Reports
The following tables summarize Perlegen's genome-wide DNA variation study in 15 commonly used strains of inbred laboratory mice by strain and by chromosome.
Strain Summary
The following table summarizes the sequence and SNP information generated for each of the 15 inbred strains used in this study. It displays the amount of sequence submitted to the NCBI Trace Archive, the amount of sequence analyzed for variation from other strains, and the number of genotypes called per strain at polymorphic sites discovered in this project and submitted to dbSNP.
For a more detailed review of the strains used in this study, visit The Jackson Laboratory website.
| Strain Name1 | Seq. Submitted (MB)2 | Seq. Analyzed for SNPs (MB)3 | Number of Genotypes Submitted4 |
|---|---|---|---|
| 129S1/SvImJ | 1494.582 | 1494.582 | 7295599 |
| A/J | 1493.232 | 1493.232 | 7425112 |
| AKR/J | 1493.232 | 1493.232 | 7329818 |
| BALB/cByJ | 1494.582 | 1494.582 | 7367458 |
| BTBR T+ tf/J | 1494.582 | 1494.582 | 7320897 |
| C3H/HeJ | 1494.455 | 1494.455 | 7239689 |
| CAST/EiJ | 1494.455 | 1494.455 | 6996315 |
| DBA/2J | 1494.455 | 1494.455 | 7266829 |
| FVB/NJ | 1494.455 | 1494.455 | 7313926 |
| KK/HlJ | 1494.455 | 1494.455 | 7323248 |
| MOLF/EiJ | 1494.455 | 1494.455 | 7031328 |
| NOD/LtJ | 1494.455 | 1494.455 | 7300000 |
| NZW/LacJ | 1494.582 | 1494.582 | 7313621 |
| PWD/PhJ | 1494.582 | 1494.582 | 6949802 |
| WSB/EiJ | 1494.582 | 1494.582 | 7291655 |
2Multiple sequence reads of the same region are considered only once
3Amount of sequence scanned for SNPs
4Number of genotypes called at polymorphic sites discovered in this project
Chromosome Summary
The following table summarizes the amount of genomic sequence examined for polymorphisms, the amount of sequence submitted to the NCBI Trace Archive, and the number of SNPs identified and submitted to dbSNP, for each chromosome.
| Chromosome | Chromosome Length (MB)1 | Seq. Submitted (MB)2 | SNPs submitted3 |
|---|---|---|---|
| 01 | 197.142 | 112.043 | 725333 |
| 02 | 181.977 | 107.36 | 536890 |
| 03 | 159.872 | 90.073 | 529628 |
| 04 | 155.03 | 85.056 | 496885 |
| 05 | 154.574 | 88.022 | 520144 |
| 06 | 149.526 | 86.315 | 545009 |
| 07 | 145.228 | 77.859 | 453850 |
| 08 | 132.292 | 76.822 | 460703 |
| 09 | 124.018 | 73.39 | 373007 |
| 10 | 129.97 | 76.192 | 415665 |
| 11 | 121.799 | 75.839 | 263447 |
| 12 | 120.463 | 69.803 | 419456 |
| 13 | 121.001 | 69.361 | 424242 |
| 14 | 123.979 | 71.061 | 371159 |
| 15 | 103.549 | 61.474 | 347159 |
| 16 | 98.252 | 57.743 | 314405 |
| 17 | 95.217 | 53.778 | 291718 |
| 18 | 90.737 | 53.197 | 298383 |
| 19 | 61.321 | 36.27 | 233252 |
| M | .016 | .016 | 286 |
| X | 165.596 | 64.274 | 247018 |
| Y | 29.007 | 2.345 | 4935 |
| Unassigned4 | .64 | .311 | 2332 |
| Unmapped5 | 2.929 | 47637 |
2Sequence submitted to the NCBI Trace Archive, as mapped to NCBI Build 36. Repetitive sequence was not assayed.
3SNPs submitted to dbSNP, as mapped to NCBI Build 36.
4C57BL/6J contigs in NCBI Build 36 not assigned to a chromosome.
5Sequence assayed and SNPs found on earlier builds of the mouse genome that could not be definitively mapped to NCBI Build 36.