Screening populations for copy number variation using genotyping-by-sequencing: a proof of concept using soybean fast neutron mutants

Table 1 Breakdown of the bin filtering steps of read count datasets

	Homozygous deletions and duplications	Hemizygous deletions
Mapping quality threshold	20	35
Initial number of reads	82,923,013^a	75,841,175
Number of bins with at least 1 read	152,061	141,068
Bins removed by max-read filter	7	6
Bins removed by min-read filter	117,406^b	111,039^b
Bins removed by var./mean filter	1907	1584
Number of bins remaining	32,741	28,439
Number of reads in remaining bins	67,905,271	61,254,871

Numbers shown in this table pertain to the sequencing data obtained from the first GBS library. The read and bin counts shown come from 81 mutants and 4 controls. The same dataset was used to call homozygous deletions and duplications. Different filters were applied to the dataset used to call hemizygous deletions
^aSee Additional file 1: Figure S10 for the distribution of the number of mapped reads per individual
^bMinimum number of reads/bin = 7 for homozygous deletions/duplications and = 8 for hemizygous deletions

ISSN: 1471-2164