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Table 6 Results comparison between GT-WGS and BWA + GATK

From: GT-WGS: an efficient and economic tool for large-scale WGS analyses based on the AWS cloud service

Mutation type Unique mutation sites of GT-WGS Unique mutation sites of BWA + GATK best practice Common mutation sites Mutation sites with consistent position but different genotype
Number Proportion Number Proportion Number Proportion Number Proportion
SNP 3928 0.10% 4443 0.11% 4,067,370 (99.89%, 99.88%) 643 (0.016%, 0.016%)
INDEL 646 0.08% 675 0.08% 823,871 (99.90%, 99.89%) 197 (0.024%, 0.024%)