Detection and characterization of small insertion and deletion genetic variants in modern layer chicken genomes

BMC Genomics

Table 1 False discovery rates (FDR) for the InDels identified by next generation sequencing in 24 validation regions

InDel Set	NGS InDels	TP^a	FP^b	TN^c	FN^d	Sensitivity	Specificity	FP rate (1-specificity)	FN rate (1-sensitivity)	VR^e
Dindel	17	15	2	9,739	4	0.7895	0.9998	0.0002	0.2105	0.8824
SAMtools	17	16	1	9,740	3	0.8421	0.9999	0.0001	0.1579	0.9411
Consensus filtered⁶	15	14	1	9,740	5	0.7368	0.9999	0.0001	0.2631	0.9333

^aTP = True Positive and this refers to the number of InDels detected by both Sanger and NGS methods. ^bFP = False Positive and this refers to the number of InDels detected only by NGS. ^cTN = True Negatives and refers to the number of bases which were sequenced but not called as InDels by Sanger or NGS. ^dFN = False Negative and refers to the number of InDels detected only by Sanger. ^eVR = Validation Rate was calculated as (TP/number of NGS InDels). ^fConsensus filtered set included the common InDels detected by both SAMtools and Dindel and retained after filtration

ISSN: 1471-2164