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

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

Trait	No. of putative SNPs		No. of SNPs with Allelic imbalance
Trait	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**

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

ISSN: 1471-2164