Different start and end position after chimera

[allan_santos]

Dear all,
I’m running v4 sequencing and after perform the chimera vsearch I’ve obtained a start position at 1 and end position at 611 as you can see below, unlikely what appears in SOP (start=1, end=376).
I’m following the steps of this SOP from the beginning.
Could anyone explain why of this?
Thank you

mothur > summary.seqs(fasta=current, count=current)
Using luan.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.count_table as input file for the count parameter.
Using luan.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.fasta as input file for the fasta parameter.

Using 64 processors.

            Start   End     NBases  Ambigs  Polymer NumSeqs

Minimum: 1 604 220 0 3 1
2.5%-tile: 1 611 253 0 4 23738
25%-tile: 1 611 253 0 5 237371
Median: 1 611 253 0 5 474742
75%-tile: 1 611 253 0 6 712113
97.5%-tile: 1 611 253 0 6 925746
Maximum: 1 611 273 0 8 949483
Mean: 1 610 252 0 5

of unique seqs: 24115

total # of seqs: 949483

It took 0 secs to summarize 949483 sequences.

[pschloss]

It’s likely because you have different sequence diversity than we had in the SOP. Prior to this step you ran filter.seqs, which removes columns that only contain gaps. It would appear that either because we have different bacteria represented or differences in data quality, you have more bases in positions where we only had gaps.

Pat