Closed:How to find mismatches in an assembly

Question

[mary]

Edited: I'm using Tablet software to view my sorted BAM file and trying to set a feature to show mismatch threshold at which bases on an alignment coverage track are marked. i. e. if the percent of nucleotide differs from the consensus sequence is greater than that % of reads, it would be marked as a feature.

for this, I need to create a BED or GFF3 file from the sorted BAM file, which has the place of every nucleotide in every contig where the nucleotides of mapped reads has variation greater than the defined percent.

for example, I want to have a bed file with a list of positions where 30% of reads has a nucleotide variation from what is assigned to the assembled contig.