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Mouse Report

Mouse Report. Brian S. Yandell 5 oct 2007. SNP data matrix. ## snp (4853 x (8 + 566)) Raw SNP genotypes ## Assay.Id Internal Affy ID ## External.Id External ID: rs + number ## Target.Allele bases to compare: A/C, A/T, ...

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Mouse Report

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  1. Mouse Report Brian S. Yandell 5 oct 2007

  2. SNP data matrix ## snp (4853 x (8 + 566)) Raw SNP genotypes ## Assay.Id Internal Affy ID ## External.Id External ID: rs + number ## Target.Allele bases to compare: A/C, A/T, ... ## Genome.Map Mouse NCBI Build 32 ## Chrom.Name 1:19, X ## Chrom.Position Converted below to Mb. ## Gene All are missing (proprietary?). ## Assay.Call.Rate.. % of samples with calls? ## tid28437_Mouse2272_B6_Male SNP Entries for 566 mice Target.Allele SNP Entries A/A 0 A/C 1 C/C 2 ? 5

  3. overview • 566 mice B6 BTBR F1 F2 MouseKitControl 755356 0 0 0 0 1 Female 1 2 2 264 0 Male 2 2 2 290 0 • score for microarray step 1.Best 2.HetMaleX 3.LowCallRate 4.NonSegMismatch 514 12 9 8 5.CageSex 6.BadGenos 7.NoGenos 8.NotF2 2 6 3 12

  4. SNPs for Parents ## Good SNPs have the following parent patterns (ignoring 5=NA): ## B6 F1 BTBR ## 0 0 0 non-segregating ## 2 2 2 ## ## 0 1 2 segregating ## 2 1 0 ## ## 0 2 2 segregating--X males with BTBR mothers ## 2 0 0 ## ## 0 0 2 segregating--X males with B6 mothers ## 2 2 0 Non-Segregating Segregating Het B6/BTBR Match 2747 2034 Mismatch 12 16 Total 2759 2050 44

  5. SNPs for F2s Segregating Parents F2 recoding B6 F1 BTBR 0 1 2 0 1 2 1 2 3 2 1 0 3 2 1 X males 0 2 2 1 7 2 2 0 0 2 7 1 Non-Segregating Parents F2 recoding B6 F1 BTBR 0 1 2 0 0 0 456 2 2 2 65 4 F2 codes 1,2,3 useful for gene mapping 4 valid but not informative 5,6,7 invalid

  6. genotype color scheme Blue 1 B6 Purple 2 het Green 3 BTBR Gray 4 correct noninformative SNP Red 5 het coding for noninformative SNP Orange 6 opposite for noninformative SNP White NA missing value

  7. SNPs for F2s F2 mice Mismatch with parents for non-segregating markers 0 1 2 3 4 5 6 7 189 140 88 44 28 14 8 8 8 9 10 11 12 13 15 18 8 7 4 5 2 2 1 1 21 24 27 31 35 38 41 44 1 1 1 1 2 1 1 1 47 66996 1120 1134 1188 1225 1269 1 1 1 1 1 1 1 1 X SNP Het errors for F2 males 40 X chr SNPs had Mismatch for at least one F2 male 12 F2 male mice had at least 4 X chr SNP mismatch

  8. double crossovers per mouse • DC1: SNP differs from both flanking SNPs 0 1 2 3 4 5 6 7 8 9 31 46 85 95 78 61 44 35 18 15 10 11 12 13 15 16 17 18 19 23 11 6 8 4 3 3 2 3 3 1 25 29 32 33 41 55 128274 310 350 1 1 2 1 1 1 1 1 1 1 356 363 390 1 1 1 • DC2: SNP to flanking SNP: B6 to BTBR 0 1 2 3 4 5 6 7 16 221 229 161 96 46 17 7 2 1 1 1 339 341 345 346 408 1 1 1 1 1

  9. R/qtl cross object > summary(B6BTBR07) F2 intercross No. individuals: 545 No. phenotypes: 121 Percent phenotyped: 100 100 100 100 99.8 99.8 99.8 99.8 99.8 99.8 99.8 92.8 99.8 99.6 96 99.8 99.8 99.8 95 88.4 99.8 99.8 29.4 99.8 98.9 99.8 14.1 6.6 19.3 96 99.8 17.8 99.8 99.8 23.7 24.4 10.3 99.8 99.6 99.8 27.3 2.9 36.9 98.9 37.8 21.7 99.8 99.8 99.4 99.8 99.8 99.8 99.8 99.8 98.7 99.8 99.8 99.8 87.7 99.8 99.4 99.8 98.2 99.8 99.8 16.5 99.4 99.8 50.5 99.8 99.8 99.4 99.8 99.8 23.9 99.8 99.8 99.8 86.4 100 100 100 100 100 100 100 100 75.4 100 11.6 11.6 100 100 3.7 100 100 100 100 100 2.2 100 99.6 99.6 99.6 99.6 100 100 98.2 98.2 100 98.2 100 100 100 100 100 100 100 100 99.8 100 No. chromosomes: 20 Autosomes: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 X chr: X Total markers: 2034 No. markers: 155 132 158 123 123 100 106 93 92 122 121 116 115 91 102 66 59 91 49 20 Percent genotyped: 99.4 Genotypes (%): AA:24.9 AB:49.9 BB:25.2 not BB:0 not AA:0 Warning message: Invalid genotypes on X chromosome: Observed genotypes: 1 3 2 NA in: summary.cross(B6BTBR07)

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