4. GS De Novo Assembler and GS Reference Mapper Appendices
:
4.10 Annotation File Formats
: 4.10.3 snp130.txt File Format
4.10.3
snp130.txt File Format
The Golden Path file snp130.txt is a tab-delimited text file consisting of 18 fields. All fields are required, including the bin field. The value of the bin field is ignored, but must be present.
Field
Description
bin
Indexing field
chrom
Reference sequence chromosome or scaffold
chromStart
Start position in chrom
chromEnd
End position in chrom
name
Reference SNP identifier or Affy SNP name
score
Not used
strand
+ or - for strand
refNCBI
Reference genomic from dbSNP
refUCSC
Reference genomic from nib lookup
observed
The sequences of the observed alleles from rs-fasta files
molType
'unknown', 'genomic' or 'cDNA'
class
'unknown', 'single','in-del', 'het','microsatellite', 'named', 'mixed', 'mnp', 'insertion' or 'deletion'
valid
'unknown', 'by-cluster', 'by-frequency', 'by-submitter', 'by-2hit-2allele' or 'by-hapmap'
avHet
The average heterozygosity from all observations
avHetSE
The Standard Error for the average heterozygosity
func
The functional category of the SNP (coding-synon, coding-nonsynon, intron, etc.)
locType
'range', 'exact', 'between', 'rangeInsertion', 'rangeSubstitution' or 'rangeDeletion'
weight
The quality of the alignment
