Reads lost after processing

[manuelaraujo1000]

Hi,

I seek help understanding the final output. I have processed a file with around 2000 sequences, with the objective of locating a SNP in a 10 nucleotide region. The software was perfect to locate this SNP, however it seems some reads which spanned this region have been dropped during the analysis. Attached I send two of the output files the pos.txt has the correct number of reads, however in the hap.txt these are reduced and for the read.txt this is the same. I would like to understand why this is happening.

Thanks in advanced.