Formatted data from soybase & other helper tables for oil mapping populations 201 and 202
LinkageMap50k.csv
Linkage map from the 50k SNP chip from the Williams 82 x PI479752 (WP) population
- SNP.ID.Simple: Shortened SNP name from the Glyma1 assembly
- Glyma1.01.Chromosome: Chromosome from the Glyma1 assembly
- Glyma1.01.Coordinate: BP position in the Glyma1 assembly
- Wm82.a2.v1.Chromosome: Chromosome from the Wm82.a2 assembly
- Wm82.a2.v1.Coordinate: BP Position from the Wm82.a2 assembly
- WP.Linkage.Group: Linkage group in the linkage map from the Williams 82 x PI479752 (WP) population
- WP.linkage.position: Position in the linkage map (cM) from the Williams 82 x PI479752 (WP) population
LinkageMap6K
Linkage map from the 6k SNP chip for a Wyandot’ × PI 567301B population
- Reference.SNP.ID.rs:Reference SNP id
- Submitted.SNP.ID.ss: Submitted SNP id
- SNPName.Glyma.Wm82.a1: SNP name in the Glyma Wm82 version a1
- SNPName.Glyma.Wm82.a1.short: Short SNP name in the Glyma Wm82 version a1
- SNPName.Glyma.Wm82.a2: SNP name in the Glyma Wm82 version a2
- SNPName.Glyma.Wm82.a2.short: Short SNP name in the Glyma Wm82 version a2
- Chromosome: Chromosome label
- Position.Glyma1: SNP position in the Glyma1 assembly
- Position.Glyma2: SNP position in the Glyma2 assembly
- Genetic.position.cM: SNP position on the linkage map in cM
SNPChip50KData.csv Various descriptive and positional data for 50K SNPs from two populations
- ss.ID: Submitted SNP ID
- SNP.ID: SNP Name in the Glyma1 assembly
- Glyma1.01.Chromosome/Coordinate: Chromosome and BP position of the SNP in the Glyma1 assembly
- WM82.a2.v1.Chromosome/Coordinate: Chromosome and BP position of the SNP inthe Wm81.a2.v1 assembly
- Wm82.a2.v1.Gene.ID/Gene.Regions: Gene IDs for SNPs in the Wm82.a2.v1 assembly
- WP/EW.Linkage.Group/Linkage.Position: Genetic linkage group of the SNP in the Williams 82 x PI479752 (WP)/ Essex x Williams (EW) populations
SNPChip50KMetaData.csv
Various quality statistics for SNPS, used in the development of the 50K SNP chip.
- SNP.ID: SNP name
- Chromosome: SNP chromosome
- Coordinate: BP Position within chromosome
- Williams.82.allele: Primary allele
- Alternative.allele: Alternative allele
- sequence.flanking.SNP_60bp: SNP flanking sequence
- Bead.type.success.Y_N: Bead success? (Yes/no)
- Priority.group/SNP.score/Index.score: SNP quality measures
- Polymorphism: Y/N indicator of polymrphism for a marker
- Position.in.gene: Posision in a gene (if available)
- MAF.Elite/G.Max/G.Soja/Landrace.Elite.and.G.Soja: MAF in elite, landrace, and wild soybean populations
SoySNPConcensus_LPmerge.csv
Concensus map created from the 50K and 6K linkage maps using the LPmerge R package
- SNP: SNP Name
- LG: Linkage group/chromosome
- Pos_BP: Base Pair position of the SNP within the linkage group
- Pos_Bin1: cM position when a interval size of 1 cM is used between bins
- Pos_Bin2: Interval size of 2 cM
- Pos_Bin3: Interval size of 3 cM
EntryPlantNumberConversion.csv
File to convert between plant numbers and entries for oil mapping populations 201 and 202
- Population: WHich population does the line belong to
- Row: Entry
- Cross: Parent cross
- PlantNo: Plant number
SoybaseQTL.csv
Positions of QTL on the GM Composite genetic linkage map from soybase.
ExpectedLGSizes.csv
Expected LG sizes in cM from four linkage maps.
ConsensusMapWithPositions.csv
SNP markers from the GM Consensus 4.0 map along with physical positions on the Wm82.a2 assembly.
Wm82.a4.v1_to_Correspondence_Full.csv
Gene name lookup table to match gene names between v4 to v1 and v2 of the soybean genome. Downloaded from this page on soybase.
SoybaseLGAssignments.csv
LG names to chromosome number conversion table from SoyBase.
sbSNPConversion.csv
A table to convert the names of SNPs on the beadchip to dbSNP ids.
PI_to_common_name_conversion.csv
PI numbers to common names from GRIN for many soybean accessions. File downloaded from here