Table 1.
Summary of SNP mapping from Celera, WI, and GNF data
| Overlap with other data sets
|
||||||||
|---|---|---|---|---|---|---|---|---|
| Sourcea | All SNPs | Laboratory inbred strains | Mapped SNPs | Inconsistently mapped SNPs | SNPs per 100 kb | Celera | WI | GNF |
| Celerab | 70,795 | C57BL/6J, 129S1/SvlmJ, A/J, DBA/2J, 129X1/SvJ | 68,848 (97%) | 306 (0.4%) | 75 | — | 835 (1.2%) | 25 (0.04%) |
| WIc | 2347 | C57BL/6J, 129S1/SvlmJ, C3H/H3, BALB/cByJ | 2347 (100%) | 0 (0%) | 2.6 | 835 (35.6%) | — | 1 (0.04%) |
| GNFd | 477 | C57BL/6J, A/J, BALB/cByJ, AKR/J, DBA/2J, 129S1/SvlmJ, C3H/He | 391 (82%) | 0 (0%) | 0.4 | 25 (6.4%) | 1 (0.2%) | — |
All SNP data were obtained from the Mouse Phenome Database at the Jackson Laboratory (http://www.jax.org/phenome).
Celera SNPs were obtained from the file mpd 147.zip in the project “Celera Genomics SNPs.” As described in Wiltshire et al. (2003), SNPs in the Celera data set were discovered from Celera Assembly R13 in 2003. In this study, SNPs with inconsistent mapping order on the Celera and MGSCv3 assembly were identified and excluded from haplotype analysis. There is no additional filtering other than that.
WI SNPs were obtained from the file mpd127big.zip in the project “MIT mouse SNP data-2.”
GNF SNPs were obtained from the files mpd 133strains.zip and mpd133loc.zip in the project “GNF mouse SNP data.”