Skip to main content

Advertisement

Table 3 Concordant polymorphisms for QTL that were clustered in two or more than two groups

From: Concordance analysis for QTL detection in dairy cattle: a case study of leg morphology

QTL indiv conc intg intr down up other full genes
2 groups
4 58 42 4 37 0 1 0 0 VPS13B, OSR2
6 64 15 0 12 3 0 0 0 MAP2K6
9 59 8 0 7 1 0 0 1 ADARB2, miRNA
11 65 27 24 0 3 0 0 0 5S rRNA
12 43 3 3 0 0 0 0 0 -
14 58 102 100 0 0 2 0 22 RAP1GAP2
15 59 340 115 197 0 28 0 6 BTRC, LBX1
18 59 63 63 0 0 0 0 1 -
19 59 35 0 35 0 0 0 0 COL11A1
20 59 65 65 0 0 0 0 0 -
>2 groups
1 40 327 265 42 4 12 4 0 SLC35B3, EEF1E1, BLOC1S5, TXNDC5, 5S rRNA, BMP6, U6, DSP, RIOK1, CAGE1, SSR1, RREB1
3 37 52 40 8 2 1 1 0 TANC2, ACE3, SCN4A, ICAM2, ERN1, miRNA
7 46 411 197 126 39 47 2 0 PCBP3, 5S rRNA
13 34 31 7 21 3 0 0 3 BRD3, EHMT1, ARRDC1, MRPL41, WDR85, PNPLA7, NELF, EXD3
17 29 187 113 71 3 0 0 97 KAT6B, KCNMA1, pseudogene
  1. indiv = number of concordant polymorphisms for the QTL used in the concordance analysis, the average number of individuals with known QTL status and sequence quality score ≥ 20; conc = number of concordant polymorphisms; intg = number of intergenic concordant polymorphisms; intr = number of intronic concordant polymorphisms; down = number of downstream concordant polymorphisms; up = number of upstream concordant polymorphisms; other = number of other concordant polymorphisms including 3′ prime variants, synonymous variant, splice variants and non-coding exon variants; full = polymorphisms in complete concordance; and names of the genes containing concordant polymorphisms.