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Table 1 Summary of putative SNPs and SNPs showing allelic imbalances identified by SAMtools and GATK for each trait

From: Identification of SNPs associated with muscle yield and quality traits using allelic-imbalance analyses of pooled RNA-Seq samples in rainbow trout

Trait No. of putative SNPs No. of SNPs with Allelic imbalance
SAMtools/Popoolation2 GATK SAMtools/Popoolation2 GATK
    0.5/2.0 0.0/1.0 0.5/2.0 0.0/1.0
Fat% 59,032 38,808 662 406 877 270
Shear 60,309 38,960 910 488 1152 261
Muscle% 61,117 42,383 1321 116 1507 76
Whiteness 64,636 44,460 1011 347 1283 298
WBW 59,711 39,993 1166 93 1456 64
Total # SNPs 304,805 204,604 5070 1450 6275 969
Total # SNPs non-redundant 87,066 59,112 4962 4798
Total Common SNPs 50,885 1829
  All putative SNPs(MAF > 0.05) =95,234* Total No. of SNPs with allelic imbalance = 7930**
  1. Allelic imbalances were calculated at >2 for amplification and <0.5 for loss of heterozygosity. SNPs explicitly existing in only the high or low phenotypic group are indicated in the table by the 0.0/1.0 ratio. * 59 SNPs were multi-allelic, showing different alleles in association with different phenotypes. ** 1 SNP was multi-allelic showing different alleles predicted by different pipelines