TABLE 5.
Amino acid | Codon change (count in CRS) | No. of observed changesa to/from | P | P′ |
---|---|---|---|---|
Ala | GCG (8) to GCA (80) | 9/5 | 3 × 10−7 | 2 × 10−4 |
GCU (43) to GCC (123) | 19/8 | 2 × 10−6 | 0.002 | |
Asn | AAU (32) to AAC (132) | 13/13 | 7 × 10−4 | 0.042 |
Asp | GAU (15) to GAC (51) | 12/5 | 2 × 10−4 | 0.004 |
Gln | CAG (8) to CAA (82) | 7/9 | 0.001 | 0.018 |
Glu | GAG (24 )to GAA (64) | 18/10 | 4 × 10−4 | 0.046 |
Gly | GGG (34) to GGA (67) | 44/37 | 0.005 | |
GGU (24) to GGC (87) | 11/12 | 0.014 | ||
Ile | AUU (124) to AUC (196) | 38/26 | 0.002 | |
Leu | CUG (45) to CUA (276) | 39/59 | 1 × 10−7 | 0.006 |
UUG (19) to CUG (45) | 4/3 | 0.099 | ||
UUA (73) to CUA (276) | 28/18 | 4 × 10−8 | 2 × 10−4 | |
CUU (65) to CUC (167) | 25/18 | 1 × 10−4 | 0.032 | |
UUG (19) to UUA (73) | 14/11 | 5 × 10−4 | 0.048 | |
Lys | AAG (10) to AAA (85) | 6/10 | 0.004 | |
Met | AUG (40) to AUA (167) | 31/29 | 5 × 10−6 | 0.008 |
Phe | UUU (77) to UUC (139) | 24/17 | 0.006 | |
Pro | CCG (7) to CCA (52) | 14/10 | 1 × 10−5 | 3 × 10−4 |
CCU (41) to CCC (119) | 22/14 | 3 × 10−4 | 0.008 | |
Ser | AGU (14) to AGC (39) | 7/3 | 0.02 | |
UCG (7) to UCA (83) | 5/10 | 0.02 | ||
UCU (32) to UCC (99) | 14/7 | 9 × 10−5 | 0.008 | |
Thr | ACU (52) to ACC (155) | 27/16 | 6 × 10−7 | 0.002 |
ACG (10) to ACA (134) | 24/11 | 9 × 10−16 | 9 × 10−13 | |
Try | UGG (11) to UGA (93) | 18/36 | 5 × 10−4 | 0.031 |
Tyr | UAU (46) to UAC (89) | 22/17 | 0.01 | |
Val | GUU (31) to GUC (48) | 15/6 | 0.008 | |
Total | NNG (223) to NNA (1256) | 229/237 | 4.6 × 10−52 | 5.3E-19 |
NNU (596) to NNC (1444) | 249/162 | 2.8 × 10−34 | 1.8E-27 | |
ND6 | NNG (62) to NNA (35) | 14/19 | 0.03 inverse | |
NNU (72) to NNC (6) | 10/6 | 1.1 × 10−3 |
P is a chi-square probability assuming equal rates of codon exchange and estimates the difference from the expected number of changes, given the codon frequencies in the reference mtDNA sequence (Andrews et al. 1999). P′ is binomial probability taking into account additional transitional biases observed over the whole mitochondrial genome favoring transitions G to A over A to G and T to C over C to T by factors of 2.33 and 1.93, per respective nucleotides.
Number of changes corresponds to mutations (including multiple hits per site) inferred in phylogenetic analysis (Figure 1).