False-positive SNVs were excluded using the following thresholds: Fisher's exact test P < 0.05, coverage ≥10×, Phred base quality score ≥20, minimum variant allele frequency ≥20% and high-quality reads supporting variants allele ≥4.
Parameters for SNP analysis using CLC Genomics Workbench: max # of gaps and mismatches 2, minimum average of quality of surrounding bases 15, minimum quality of central base 20, minimum coverage 1, minimum variant frequence 35%.
SNP calling parameters were set to minimum coverage = 5, and minimum variant frequency = 0.2.
A position to make a call, the following criteria have to be satisfied: (1) minimum read depth (2)minimum number of reads with variant allele (3) minimum variant allele frequency (4) minimum base quality (5) max p value.
Single-base substitutions were detected based on minimum total coverage of 10 and minimum variant coverage of 3.
Minimum variant frequency was set to zero, to allow comparison with ShoRAH.
The working dataset of high coverage contigs was screened for SNPs using the CLC Genomics Workbench v. 5.5 (minimum coverage 8×, minimum variant frequency 10%, minimum number of reads per allele = 2, minimum central quality 20).
Parameters were as follows: neighborhood radius = 5, maximum gap and mismatch count = 2, minimum neighborhood quality = 15, minimum central quality = 20, minimum coverage = 10, and minimum variant frequency = 35.0.
The working data set of high coverage contigs was screened for SNPs using the CLC Genomics Workbench v. 5.5 (minimum coverage 8×, minimum variant frequency 10%, minimum reads per allele = 2, minimum central quality 20).
Within the high coverage data set, 8,339 contigs contained SNPs that fell within our detection parameters (minimum coverage 8×, minimum variant frequency 10%, minimum reads per allele = 2, minimum central quality 20).
