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Table 2 QTLs identified in R/qtl analyses

From: Heart disease in a mutant mouse model of spontaneous eosinophilic myocarditis maps to three loci

Cross
(#HD / #Unaffected)
Chr position
(@ peak SNP)
LOD Score % Variance Explained Level of Significancea Haplotype-defined interval
Chr: Mb range (size of interval)
D2.HD-N2
(19 / 6)
5:147147276 3.32 43.2 suggestive 5:143159090–151734385
(8.58 Mb)
D2.HD-F2
(16 / 16)
5:144329217–147894899
(3.57 Mb)
SJ.HD-N2
(16 / 17)
5:148558183 4.88 47.4 highly significant
(Emhd1)
5:129525220–151734385
(22.21 Mb)
SJ.HD-F2
(22 / 22)
5:145128608–147778059
(2.65 Mb)
17:21456192 7.51 52.9 highly significant
(Emhd2)
17:15358323–23816187
(8.46 Mb)
17:35308100 6.89 49.6 highly significant
(Emhd3)
17:31471362–46058209
(14.59 Mb)
SJ.HD-N2 + F2
(38 / 39)
1:176044015 4.12 21.3 significant 1:172969406–194625219
(23.59 Mb)
5:146601763 5.79 28.6 highly significant
(Emhd1)
5:143159090–151734385
(8.58 Mb)
17:17933928 6.53 35.1 highly significant
(Emhd2)
same as F2
17:35308100 7.43 highly significant
(Emhd3)
same as F2
  1. All genomic positions are based on mm10 (GRCm38; Build 38). Genotyping of > 143,00 SNPs was performed by GeneSeek (Lincoln, NE) using the GigaMUGA SNP panel. Separate QTL analyses were run for each cross using R/qtl [16, 17] after applying argyle routines for quality checks [18]. Combined SJ crosses were analyzed as an F2 model (0,1,2), accepting the limitations. a Significance was determined using 1000 permutations of the corresponding dataset. QTL intervals were determined using haplotype analysis, in which we identified the proximal and distal crossovers that best correlated the genotype with phenotype