snp-search: simple processing, manipulation and searching of SNPs from high-throughput sequencing

BMC Bioinformatics

Table 1 ST315 clade unique SNP information - typical snp-search output for -u option

Pos	Ref base	SNP	syn/non-syn	Gene annotation	Pseudo gene?	AA orig	AA change	CH?	CP?	CS?
16387	A	G	syn	putative amino acid permease	No
512693	A	G	non-syn	putative dipeptidase	No	T	A	No	Yes	No
924493	T	C	non-syn	putative sugar ABC transporter (ATP-binding protein)	No	S	P	No	Yes	No
1108998	G	T	non-syn	putative N-acetylglucosamine-6-phosphate isomerase	No	A	S	Yes	Yes	No
1186147	C	T	syn	putative amino acid ABC transporter (ATP-binding protein)	No
1573272	T	C	non-syn	putative sucrose operon repressor	No	L	S	Yes	Yes	Yes
1817279	C	T
1868362	T	C

Last two empty cells indicate the SNP has occurred in a non-CDS region therefore having no further information. Syn: synonymous, Pos: position of SNP in reference genome, AA: Amino acid, orig: original, CH: change in hydrophobicity, CP: change in polarity, CS: change in size.

ISSN: 1471-2105