PREFIX.pergeno.aa_mutations.csv

This file includes amino acid changing annotations for each proteins.

files are in csv format (with \t as separator). Transposed table looks like:

protein_id	ENSP00000437362	ENSP00000446015	ENSP00000450505	ENSP00000451203	ENSP00000452431
protein_id_fasta	ENSP00000437362.1	ENSP00000446015.1	ENSP00000450505.1	ENSP00000451203.1	ENSP00000452431.1
seqname	14	14	14	14	14
strand	+	+	+	+	+
frameChange
stopGain
AA_stopGain
stopLoss
stopLoss_pos
n_variant_AA	1.0	2.0	2.0	1.0	1.0
n_deletion_AA
n_insertion_AA
variant_AA	F70S(14-21888371-T-C)	P50Q(14-21924450-C-A);Q76E(14-21924527-C-G)	E77K(14-21979008-G-A);S78G(14-21979011-A-G)	S103L(14-22086905-C-T)	T25P(14-22124030-A-C)
insertion_AA
deletion_AA
len_ref_AA	113	116	113	121	109
len_alt_AA	113.0	116.0	113.0	121.0	109.0

Columns:

• protein_id: protein_id used in perGeno analysis
• protein_id_fasta: protein id that is stored in fasta file
• seqname: chromosome name
• strand: strand of proteins in chromosome
• frameChange: if there is a frame change mutation
• stopGain: if there is a stopgain mutation
• AA_stopGain: amino acid (AA) that is mutated to a stop codon
• stopLoss: if there is a stoploss mutation
• stopLoss_pos: position of stoploss in protein sequence
• nonStandardStopCodon: for proteins with mutations, if translation is stop and a position that is not a stop codon
• n_variant_AA: count of AA substitution
• n_deletion_AA: count of AA deletion
• n_insertion_AA: count of AA insertion
• variant_AA: substituted AAs
• insertion_AA: inserted AAs
• deletion_AA: deleted AAs
• len_ref_AA: length of provided protein
• len_alt_AA: length of changed protein

Note: some of those columns may be empty.