In a recent run of SRST2 for MLST (E. coli no. 1 ST database), one of my isolates has an unambiguous sequence type reported (i.e. ST 73, no question marks or anything like that), but in the 'mismatches' column, "allele_#/trun" is reported. I went back to the pileup, however, and the complete allele is covered by reads (no SNPs, minimum read depth above threshold, minimum % of allele covered, etc.).
Why would/could SRST2 report a truncation if the entire allele is present and covered by sufficient read depth?
Any help in understanding this issue would be most appreciated.
Hello,
In a recent run of SRST2 for MLST (E. coli no. 1 ST database), one of my isolates has an unambiguous sequence type reported (i.e. ST 73, no question marks or anything like that), but in the 'mismatches' column, "allele_#/trun" is reported. I went back to the pileup, however, and the complete allele is covered by reads (no SNPs, minimum read depth above threshold, minimum % of allele covered, etc.).
Why would/could SRST2 report a truncation if the entire allele is present and covered by sufficient read depth?
Any help in understanding this issue would be most appreciated.
Thank you, Conrad