Length of filtered alignment

1

Hi community!!!
After the

mothur > filter.seqs(fasta=stability.trim.contigs.good.unique.good.align, vertical=T, trump=.)

step in mothur, I am seeing the “length of filtered alignment” in my different data sets differ. In different cases it is 468, 464 or 451. Whereas the length of the original alignment is constant, 13425. I have seen the ''Length of filtered alignment" in SOP is 376 where the length of the original alignment is same.

Why am I getting this dscrepancy in “Length of filtered alignment”?

Length of filtered alignment: 464
Number of columns removed: 12961
Length of the original alignment: 13425
Number of sequences used to construct filter: 168379

Length of filtered alignment: 451
Number of columns removed: 12974
Length of the original alignment: 13425
Number of sequences used to construct filter: 160162

Length of filtered alignment: 468
Number of columns removed: 12957
Length of the original alignment: 13425
Number of sequences used to construct filter: 201192

Thanks & Regards,
DC7

2

since you are using vertical=t, the exact columns that are removed will depend on what phyla are present in that exact set of samples. Also remember that you can’t compare your numbers directly to the SOP numbers because you are working with a different variable region.

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3

I’m using V4 region (same as SOP).

4

if you a missing some lineages that have different indels, then the positions that are 100% gaps are removed. The 13000+ length is if you try to align all living things, basically. Or at least representatives of most lineages (as SILVA “is”).

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