Lettuce Genetic Map - RIL213 SPP Consensus - RECORD_Win version

AffyLettChip_TI_ProbeSet_NativeAlien_12841.4LC.RECORD_Win.fa - FASTA file with 12841 mapped lettuce sequences on Affy Chip.
Each FASTA header has primary ID for original sequence and associated with it four letter code, for example: "CLS_S3_Contig2 AYYE".
FASTA header has map position (linkage group and cM distance) for each sequence (unigene).

Map data file name explanation:
SalSerRil213_LG1_masked_RW_.map Map with selected markers constructed with RECORD_Win
SalSerRil213_LG1_masked_.Loc Locus file with selected markers
SalSerRil213_LG1_Complete.map complete map with inserted redundant markers
SalSerRil213_LG1_Complete.Loc locus file with all markers


LG MAP DATA CheckMatrix Haplotypes Notes
Heat maps showing linkage along nine linkage groups displayed using Checkmatrix. Each chromosome is plotted in the linear order of the loci against itself and the degree of linkage between each locus indicated by a color. Red = < 0.1 cM. Yellow = 0.1 - 0.4 cM. Green = 0.4 - 0.49 cM. Blue = > 0.51 cM. The first column at the right lists the locus name. The second column indicates the genetic distance. The red and blue bars at the bottom indicate the allelic composition at each locus. Red = Salinas allele, blue = L. serriola allele; yellow = distortion towards the Salinas allele, light blue = distortion towards L. serriola allele. Small images are web links to larger versions. Distribution of haplotypes along nine linkage groups displayed vertically for 213 RILs using Checkmatrix. The RIL families are arranged along the x axis and the loci displayed in linear order along the y axis. Red = L. sativa haplotype. Blue = L. serriola haplotype. Grey = No allele called; missing data. The first column at the right lists the locus name. The second column indicates the genetic distance. The number of double cross-overs and the proportions of each haplotype are shown below each RIL. Small images are web links to larger versions.
1
SalSerRil213_LG1_masked_RW_.map
SalSerRil213_LG1_masked_.Loc

SalSerRil213_LG1_Complete.map
SalSerRil213_LG1_Complete.Loc


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2
SalSerRil213_LG2_masked_RW_.map
SalSerRil213_LG2_masked_.Loc

SalSerRil213_LG2_Complete.map
SalSerRil213_LG2_Complete.Loc


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3
SalSerRil213_LG3_masked_RW_.map
SalSerRil213_LG3_masked_.Loc

SalSerRil213_LG3_Complete.map
SalSerRil213_LG3_Complete.Loc


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4
SalSerRil213_LG4_masked_RW_.map
SalSerRil213_LG4_masked_.Loc

SalSerRil213_LG4_Complete.map
SalSerRil213_LG4_Complete.Loc


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5
SalSerRil213_LG5_masked_RW_.map
SalSerRil213_LG5_masked_.Loc

SalSerRil213_LG5_Complete.map
SalSerRil213_LG5_Complete.Loc


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6
SalSerRil213_LG6_masked_RW_.map
SalSerRil213_LG6_masked_.Loc

SalSerRil213_LG6_Complete.map
SalSerRil213_LG6_Complete.Loc


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7
SalSerRil213_LG7_masked_RW_.map
SalSerRil213_LG7_masked_.Loc

SalSerRil213_LG7_Complete.map
SalSerRil213_LG7_Complete.Loc


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8
SalSerRil213_LG8_masked_RW_.map
SalSerRil213_LG8_masked_.Loc

SalSerRil213_LG8_Complete.map
SalSerRil213_LG8_Complete.Loc


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9
SalSerRil213_LG9_masked_RW_.map
SalSerRil213_LG9_masked_.Loc

SalSerRil213_LG9_Complete.map
SalSerRil213_LG9_Complete.Loc


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Column designation on 'complete' maps:
1 - linkage group (1-9)
2 - marker ID
3 - map distance
4 - master marker (this marker was used for clean masked map construction)
5 - internal code for master marker type (M1 or M2)
6 - sequence ID on chip
7 - unigene ID
8 - type of duplicated sequence on chip (OR - original or DC - duplication control)


Unigene ID - four letter code conversion table: four_letter_code_converter.tab

Access to map construction intermediate steps and data is here

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