Genome-wide SNP discovery in walnut with an AGSNP pipeline updated for SNP discovery in allogamous organisms

BMC Genomics

Table 4 Comparison of several SNP identification criteria and ADT design scores in scorable and unscorable SNPs

SNP	Number of SNPs	ADT design score	Average quality score of reference	SNP quality score of reference	SNP mapping quality score	Read mapping depth	Folded variant frequency
Scorable	5,420	0.973 ± 0.052^(a)	54.6 ± 9.8	59.1 ± 6.8	34.0 ± 1.8	24.9 ± 15.7	0.35 ± 0.10
Unscorable	580	0.977 ± 0.047	54.5 ± 9.5	59.2 ± 6.9	34.0 ± 1.8	23.1 ± 14.1	0.35 ± 0.10
P value of t test		0.0677	0.9177	0.7894	0.8213	0.0086**	0.9896

(a) average ± standard deviation; ** represents statistical significance at a 0.01 probability level.

ISSN: 1471-2164