Supplemental Information for the file: Barley_SNP_Annotations.txt

This documentation was obtained on July 19, 2016 from the GitHub.com repository "MorrellLAB/SNPMeta"as SNPMeta_Manual.md and converted into a text file by DRUM curator Lisa Johnston.

To view the current version visit: https://github.com/MorrellLAB/SNPMeta/blob/master/SNPMeta_Manual.md. 

Tabular Output
When the --outfmt tabular option is given, SNPMeta will write tab-delimited text as output. Each row corresponds to a single SNP, and columns are various pieces of annotation information. Columns will be filled, depending on the amount of annotation information that is available for each SNP. If no data is available for a particular field, SNPMeta will write a - for that field. Some fields are mutually exclusive; that is, if one is filled, then the other will always be -. The table outputs 23 fields, which are explained below.

Field		Description
SNPName		The name of the SNP, taken from the FASTA record.
Organism	Organism from which the annotation was derived.
GenBankID	ID of the GenBank record used for annotation.
ProteinID	Protein ID of the CDS used for annotation, if applicable.
GeneShortName	Short name of the gene used for annotation, if applicable.
Position	Position of the SNP in the codon. Can take values of {1, 2, 3} if coding, and non-coding if not coding.
Downstream	How many bp downstream of the CDS the SNP lies, if non-coding.
Upstream	How many bp upstream of the CDS the SNP lies, if non-coding.
Silent		Whether or not the SNP alters amino acid sequence. Synonymous and non-coding SNPs getYes, and nonsynonymous SNPs get No.
AA1		Amino acid state present in the GenBank record.
AA2		Alternate amino acid state. May be identical to AA1, if synonymous.
GranthamScore	Score of amino acid substitution, as defined by Grantham (1974) in Science.
CDSPosition	Position of the affected residue in the CDS.
Codon1		Codon triplet present in the GenBank sequence.
Codon2		Alternate codon triplet.
AmbiguityCode	IUPAC ambiguity code that describes the two SNP states.
ProductName	Name of the CDS product, if applicable.
Notes		Messages and warnings about SNP files, or the nature of certain SNPs. Will be described in detail in the following section
RelatedGene	Short name of a related gene, found by searching through the list of BLAST hits.
RelatedOrganism	Source organism for the RelatedGene.
ContextSequence	Warnings about malformed SNP sequences.
AlignScore	Alignment score reported by needle, divided by the query sequence length in base pairs. Useful for flagging SNPs that may be called incorrectly due to low-quality alignments.
DateTime	Date and time the SNP was annotated.

The ‘Notes’ Field
A variety of messages can be written into the ‘Notes’ field. These will be elaborations on special classes of mutations, or messages about problems when annotating a particular SNP. The range of messages and their meanings are given below.
Value						Description
Empty File					The file SNPMeta tried to read contains no data.
No BLAST Hits					There were no BLAST hits for the sequence. If many SNPs have this message, it could be that either the list of target organisms is too restrictive, or there is a spelling error in the name of the organism.
No Annotations					The GenBank records returned by BLAST did not contain any annotated CDS.
SNP aligns to a gap in the GenBank sequence	When the GenBank sequence and the SNP contextual sequence are aligned, the SNP is placed over a gap in the GenBank sequence, making annotation impossible.
SNP aligns to a gap in the CDS			When the GenBank sequence and the SNP contextual sequence are aligned, the SNP is placed over a gap in the CDS. This could either be due to an alignment error, or a break in the annotated CDS.
CDS annotation has a fuzzy start		The CDS annotation in the GenBank record does not have an exact start position. This could cause issues with inferring reading frame.
SNP - Sequence Mismatch			The base in the GenBank sequence is not represented by the IUPAC ambiguity code in the SNP sequence.
Methionine mutation				The mutation changes an amino acid to a methionine, or from a methionine.
Disrupted STOP codon				The mutation changes a STOP codon to a different codon.
Premature STOP codon				The mutation creates a STOP codon before the end of the annotated CDS.