GBS-SNP-CROP: a reference-optional pipeline for SNP discovery and plant germplasm characterization using variable length, paired-end genotyping-by-sequencing data

Table 4 Comparative pipeline performances before (4A) and after (4B) depth-based genotyping criteria and population-level SNP calling filters for 150 bp paired-end GBS data from 48 accessions of Actinidia arguta

Pipeline	Number of SNPs^a	Average depth [D]^b	Reads with D ≥ 20 (%)^c	Hetero (%)^d	Homo (%)^e	Missing data (%)^f
4A. No SNP calling or genotyping filters applied^g
GBS-SNP-CROP-MR01	56,598	44.47	52.85	26.19	57.25	16.55
GBS-SNP-CROP-RG	23,564	47.39	39.00	26.10	51.09	22.80
TASSEL-UNEAK	12,905	6.98	9.61	13.93	52.12	33.94
TASSEL-GBS-mxTagL32	19,095	134.18	49.20	16.86	71.66	11.46
TASSEL-GBS-mxTagL64	25,005	34.65	35.60	19.21	65.80	14.98
4B. Depth-based genotyping criteria and population-level SNP calling filters applied^h
GBS-SNP-CROP-MR01	21,318	69.34	99.92	34.51	56.85	8.64
GBS-SNP-CROP-RG	5,471	77.11	99.85	38.31	53.29	8.40
TASSEL-UNEAK	1,160	44.70	83.62	31.66	66.61	1.73
TASSEL-GBS-mxTagL32	5,593	64.41	92.52	26.33	71.58	2.09
TASSEL-GBS-mxTagL64	8,907	51.42	78.07	27.80	69.36	2.84

^a Total number of SNPs called within each pipeline, under the indicated SNP calling filters and genotyping criteria
^b Average read depth for all SNPs across the entire population
^c Percentage of called SNPs with an average read depth of at least 20
^d Percentage of heterozygous genotype calls
^e Percentage of homozygous genotype calls
^f Percentage of missing cells (i.e. no genotype call for a given SNP*accession combination)
^g Liberal pipeline results in the absence of subsequent SNP calling or genotyping filters
^h Pipeline results after culling SNPs with less than 75 % scored genotypes, with D ≤ 4 (low depth), or D ≥ 200 (over-represented sequences). Further reduction is due to imposing stringent depth-based genotyping criteria, including a minimum read depth of 11 for homozygotes when the secondary allele count is zero, a minimum depth of 48 for homozygotes when the secondary allele count is one, a minimum depth of 3 for each allele for heterozygotes, and a read-depth ratio of the lower- to higher-depth allele greater than 0.1

ISSN: 1471-2105