Version 20110601

Method for detecting porcine cSNPs

We used the PolyPhred program to identify pig cSNPs (SNPs in cDNA) in the assemblies of PEDE ESTs. SNPs in regions of low-quality sequence data or near the end of an assembly were excluded from the candidate SNPs. To avoid errors (mainly caused during reverse transcription), the database contains only those SNPs that occurred on more than 1 read for each particular allele.

SNPs detected in PEDE assemblies

SNPs are classified by the effect on coding amino acids and the breed of origin. Clicking on the link by a data entry will list the assemblies belonging to that group.
In western breeds only In Meishan only Between western and Meishan breeds In both western and Meishan breeds Total
Synonymous or undetermined 2609 137 285 132 3163
Non-synonymous 1275 65 112 51 1503
Total 3884 202 397 183 4666