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Table 2 Measures of allelic balance for NA12878 whole genome sequencing dataset stratified by Genome-in-a-Bottle v3.3.2 confidence annotation

From: Reference flow: reducing reference bias using multiple population genomes

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
  1. 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