TABLE 2

Inferring codon changing SNPs between SM and NZB by examining SNPs between highly sequenced strains

Highly sequenced strains, e.g., C57BL/6, DBA/2, etc.
Chr 6 geneSNPiiiiiiivvviSMNZBSM and NZB are
Syn2UTRAAAGGGGGIBD
Syn2CsTTTCCC
Syn2CsGGGAAAAGNon-IBD
CCCTTT
PpargUTRAAAGGG
PpargCnTTTCCCctInferred Cn between SM and NZB
PpargCsGGGAAA
PpargCsCCCTTT
PpargCsAAAGGGGANon-IBD
TTTCCC
GGGAAA
Tsen2UTRCCCTTT
Tsen2CsCCCGGGCGNon-IBD
Tsen2CsTTTCCC
Tsen2CsGGGAAA
Tsen2CsCCCTTTTTIBD
  • Italic nucleotides indicate an alternative haplotype present in common inbred strains that can be used to infer the origin of polymorphisms from less well characterized strains. Although SM and NZB are not as well sequenced as other strains, missing SNPs between SM and NZB can be inferred by examining the haplotypes of the other strains. For the Cn in Pparg (underlined), SM is inferred to be ā€œCā€ and NZB is inferred to be ā€œT.ā€ Cs, coding synonymous; Cn, coding nonsynonymous; IBD, identical by descent.