Table 3 Base composition of discordant SNVs in percentages (mean ± standard deviation)
From: Similarities and differences between variants called with human reference genome HG19 or HG38
Type | Base | Picard | CrossMap | ||
|---|---|---|---|---|---|
HG38➔HG19 | HG19➔HG38 | HG38➔HG19 | HG19➔HG38 | ||
Position discordant SNVs | A | 23.43 ± 0.78 | 23.74 ± 0.81 | 23.32 ± 0.81 | 23.66 ± 0.80 |
T | 23.86 ± 0.67 | 24.02 ± 0.86 | 23.64 ± 0.70 | 23.89 ± 0.85 | |
G | 26.21 ± 0.71 | 25.92 ± 0.8 | 26.37 ± 0.75 | 26.06 ± 0.78 | |
C | 26.5 ± 0.81 | 26.32 ± 0.87 | 26.62 ± 0.81 | 26.35 ± 0.89 | |
G + C | 52.71 ± 1.44 | 52.24 ± 1.64 | 52.99 ± 1.49 | 52.41 ± 1.64 | |
Genotype discordant SNVs | A | 23.06 ± 1.61 | 23.07 ± 1.66 | 23.49 ± 0.88 | 23.57 ± 0.91 |
T | 23.11 ± 1.66 | 23.07 ± 1.75 | 23.59 ± 0.81 | 23.67 ± 0.93 | |
G | 26.74 ± 1.65 | 26.84 ± 1.92 | 26.79 ± 0.81 | 26.19 ± 1.16 | |
C | 27.08 ± 1.47 | 27.02 ± 1.45 | 26.13 ± 0.92 | 26.57 ± 0.67 | |
G + C | 53.82 ± 2.93 | 53.86 ± 3.13 | 52.92 ± 1.62 | 52.77 ± 1.73 | |