Table 1 Substitution rates derived from unconcatenated alignments. The table shows values obtained by averaging over individual in-frame alignments of sequence fragments. The alignments were derived from the chimpanzee BESs with and without the removal of low-quality sequence regions, annotated coding sequences retrieved from Genbank and coding sequence alignments derived from ESTs deposited in Genbank. Standard deviations from the mean are given in brackets.
From: FRAGS: estimation of coding sequence substitution rates from fragmentary data
Data Set | Codons | Codon identity | K a | K s | K a /K s |
|---|---|---|---|---|---|
BES (quality filtered) | 13930 | 0.932 | 0.012 (0.023) | 0.090 (0.520) | 0.301 (0.43) |
BES (unfiltered) | 42477 | 0.935 | 0.022 (0.021) | 0.076 (0.314) | 0.500 (0.53) |
Genbank CDSs | 25488 | 0.966 | 0.010 (0.014) | 0.028 (0.038) | 0.461 (0.55) |
Genbank ESTs | 114759 | 0.972 | 0.008 (0.002) | 0.048 (0.210) | 0.235 (0.01) |