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. 2006 Jan;172(1):373–387. doi: 10.1534/genetics.105.043901

TABLE 5.

Significant differences (P < 0.05) in mutational direction in synonymous sites

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.

a

Number of changes corresponds to mutations (including multiple hits per site) inferred in phylogenetic analysis (Figure 1).