Table 2.
Measures of allelic balance for NA12878 whole genome sequencing dataset stratified by Genome-in-a-Bottle v3.3.2 confidence annotation
| Method | REF-to-ALT | Total | # biased | # biased |
|---|---|---|---|---|
| ratio | # biased | toward REF | toward ALT | |
| High confidence | ||||
| GRCh38 | 1.0407 | 20,012 | 18,141 | 1871 |
| Major | 1.0227 | 19,837 | 15,415 | 4422 |
| RandFlow-LD | 1.0133 | 12,239 | 9512 | 2727 |
| vg | 1.0124 | 10,518 | 7971 | 2547 |
| RandFlow-LD-26 | 1.0098 | 9984 | 7489 | 2495 |
| Personalized | 1.0033 | 7024 | 4,600 | 2424 |
| Low confidence | ||||
| GRCh38 | 1.2355 | 24,798 | 20,594 | 4204 |
| Major | 1.1230 | 26,579 | 20,108 | 6471 |
| RandFlow-LD | 1.0282 | 22,190 | 15,891 | 6299 |
| vg | 1.0120 | 21,266 | 15,422 | 5844 |
| RandFlow-LD-26 | 1.0008 | 20,333 | 13,874 | 6459 |
| Personalized | 0.9750 | 16,266 | 9299 | 6967 |
| All regions | ||||
| GRCh38 | 1.0718 | 44,810 | 38,735 | 6075 |
| Major | 1.0397 | 46,416 | 35,523 | 10,893 |
| RandFlow-LD | 1.0160 | 34,429 | 25,403 | 9026 |
| vg | 1.0123 | 31,784 | 23,393 | 8391 |
| RandFlow-LD-26 | 1.0081 | 30,317 | 21,363 | 8954 |
| Personalized | 0.9981 | 23,290 | 13,899 | 9391 |
vg index includes variants with 10% or higher allele frequency in the 1000-Genomes Project GRCh38 call set. The methods are sorted by REF-to-ALT ratio in all regions