Table 3.
The mutation spectrum in dinucleotide contexts in the human genome inferred from single nucleotide polymorphismsa
| SNPs within a whole genome | SNPs within CGIs | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| No. | XX-YYb | Counts | Fraction (%) | Probability of XX (%) | Probability of YY (%) | XX-YY | Counts | Fraction (%) | Probability of XX (%) | Probability of YY (%) |
| 1. | AT-GT | 4747845 | 5.97 | 7.73 | 5.05 | CA-CG | 44879 | 7.99 | 5.60 | 9.89 |
| 2. | AC-AT | 4728528 | 5.95 | 5.03 | 7.73 | CG-TG | 44439 | 7.91 | 9.89 | 5.60 |
| 3. | CG-TG | 4191791 | 5.27 | 0.99 | 7.27 | CC-CT | 34022 | 6.06 | 12.43 | 6.56 |
| 4. | CA-CG | 4189811 | 5.27 | 7.25 | 0.99 | AG-GG | 33929 | 6.04 | 6.59 | 12.46 |
| 5. | AA-AG | 3467707 | 4.36 | 9.78 | 6.99 | AC-GC | 27555 | 4.91 | 4.26 | 12.02 |
| 6. | CT-TT | 3466696 | 4.36 | 7.00 | 9.80 | GC-GT | 26737 | 4.76 | 12.02 | 4.26 |
| 7. | TA-TG | 3326902 | 4.19 | 6.57 | 7.27 | CC-TC | 22113 | 3.94 | 12.43 | 5.65 |
| 8. | CA-TA | 3310846 | 4.17 | 7.25 | 6.57 | GA-GG | 22110 | 3.94 | 5.68 | 12.46 |
| 9. | CC-CT | 3036893 | 3.82 | 5.21 | 7.00 | CG-GG | 17020 | 3.03 | 9.89 | 12.46 |
| 10. | AG-GG | 3033929 | 3.82 | 6.99 | 5.21 | CC-CG | 16751 | 2.98 | 12.43 | 9.89 |
aCounts are shown in descending order and only for the first 10 SNPs. Full data set of all possible dinucleotide contexts can be found in Supplementary Table S3.
bXX and YY represent dinucleotide sequence context.