Table 2 Nucleotide substitution rates among the HQHom and private variants
HQHomALTACGT
REFA1401759 (4.0%)5073707 (14.6%)1455186 (4.2%)
C1589874 (4.6%)1072433 (3.1%)6151991 (17.7%)
G6155882 (17.7%)1072703 (3.1%)1591576 (4.6%)
T1460442 (4.2%)5076553 (14.6%)1401807 (4.0%)
PrivateALT
ACGT
REFA561 (3.8%)1161 (7.8%)720 (4.8%)
C1183 (7.9%)519 (3.5%)3323 (22.3%)
G3275 (22.0%)502 (3.4%)1179 (7.9%)
T763 (5.1%)1162 (7.8%)569 (3.8%)
  • A tabulation of reference (REF) and alternative (ALT) allele at SNPs variant sites for high-quality homozygous (HQHom) variant calls and for SNP variants that occur uniquely in one CC strain (private). The pattern of substitutions shows a high proportion of C-to-T and G-to-A substitutions and a transition–transversion ratio of ∼2.