SOAPsv

[…] stop codons or splice sites. snps in coding sequences were annotated as synonymous or non-synonymous. go or pfam annotation of genes was also conducted., structural variations were detected using soapsv (version 1.02), for indel (more than 5 bp in length), replication, reversion, transposition, and other variations. the minimum read depth was set to 3., we first calculated the distances […]

[…] reference and unmapped reads. average sequencing depth and coverage were calculated using the alignment results.20 the mapped reads were then used to detect snps, indels, and svs using soapsnp and soapsv software with default parameter settings.20–22 the snps identified were filtered based on the following stringent criteria: no less than two times for coverage depth (no less than three times […]

[…] covered approximately 84.8% of the reference genome (84%–85.99%), indicating a close relationship between the samples and cultivar 9311., snps, indels, and svs were then examined with soapsnp11 and soapsv using a conservative quality filter pipeline [14], yielding 267,383 snps from the genome of ir24, 288,764 snps from that of mh63, and 259,862 snps from that of sh527 (table 3, […]