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. 2014 Feb 11;9(2):e88380. doi: 10.1371/journal.pone.0088380

Table 4. Results of single-marker (GenABEL) and Bayesian (GenSel) genome-wide association analysis for susceptibility to MAP infection in Jersey cattle (combined data, N = 1,069)1.

SNP BTA5 Position6 A17 A28 Effect B (SE)9 P-value10 Q.2 (Cases)11 Q.2 (Controls)12 GenSel Rank13 Window (SNPs)14 %GV15 P> avg.16 Model freq.17
Common SNPs 2
ARS-BFGL-NGS-11887 23 27 776 075 A G –0.077 (0.02) 8.5×10−5 0.35 0.44 1 2199 (18) 3.21 0.29 0.23
Hapmap45793-BTA-114539 11 93 027 457 A T 0.081 (0.022) 1.3×10−4 0.32 0.25 6 1318 (8) 1.47 0.15 0.16
ARS-BFGL-NGS-92339 23 19 397 902 C A –0.10 (0.027) 1.5×10−4 0.12 0.18 10 2191 (18) 0.99 0.12 0.09
ARS-BFGL-NGS-109837 3 100 901 542 A C –0.072 (0.020) 1.6×10−4 0.43 0.51 2 399 (18) 2.12 0.19 0.15
BTA-56690-no-rs 23 44 458 259 A G –0.109 (0.030) 1.8×10−4 0.10 0.15 19 2216 (18) 0.59 0.08 0.04
Hapmap53765-ss46526662 3 107 097 209 G A –0.07 (0.020) 2.9×10−4 0.33 0.41 5 406 (13) 1.52 0.12 0.08
ARS-BFGL-NGS-20015 11 92 692 190 G A 0.071 (0.020) 3×10−4 0.43 0.35 4 1317 (15) 1.56 0.16 0.08
BTB-00148619 3 106 442 016 A G –0.069 (0.020) 3.1×10−4 0.36 0.45 9 405 (15) 1.02 0.11 0.09
ARS-BFGL-NGS-100555 17 57 131 089 A G 0.07 (0.020) 3.9×10−4 0.42 0.33 7 1818 (16) 1.28 0.13 0.1
ARS-BFGL-BAC-35219 23 29 316 835 G A –0.085 (0.025) 4.0×10−4 0.17 0.23 20 2201 (9) 0.57 0.07 0.04
BTA-75232-no-rs 5 10 104 621 G A –0.066 (0.010) 4.8×10−4 0.45 0.54 11 554 (14) 0.93 0.1 0.1
ARS-BFGL-NGS-26988 3 6 183 874 G A –0.081 (0.024) 4.8×10−4 0.18 0.24 18 305 (11) 0.62 0.07 0.06
ARS-BFGL-NGS-95270 25 19 724 505 G A –0.073 (0.022) 5.1×10−4 0.25 0.52 3 2308 (13) 1.57 0.16 0.08
BTA-30686-no-rs 6 60 692 672 A C 0.068 (0.020) 5.4×10−4 0.42 0.34 12 727 (10) 0.82 0.1 0.09
ARS-BFGL-NGS-117495 3 36 531 738 C A 0.069 (0.020) 5.2×10−4 0.40 0.32 14 335 (5) 0.72 0.08 0.08
Hapmap51790-BTA-103080 3 101 076 596 A G –0.067 (0.020) 5.6×10−4 0.40 0.48 13 400 (12) 0.79 0.09 0.05
SNPs (GenABEL only) 3
ARS-BFGL-BAC-18843 17 26 318 464 A G –0.194 (0.051) 9.0×10−5 0.02 0.06 - - - - -
ARS-BFGL-NGS-38764 13 77 546 073 G A –0.183 (0.052) 2.7×10−4 0.02 0.05 - - - - -
BTB-01324240 13 1 867 669 A G –0.161 (0.047) 4.1×10−4 0.03 0.06 - - - - -
BTA-22128-no-rs 6 13 040 713 A G –0.116 (0.035) 5.8×10−4 0.06 0.11 - - - - -
SNPs (GenSel only) 4
BTB-00643802 16 48 725 717 - - - - - - 8 1727 (17) 1.17 0.11 0.03
ARS-BFGL-NGS-2973 3 102 289 610 - - - - - - 15 401 (12) 0.69 0.07 0.04
ARS-BFGL-NGS-31524 23 50 747 363 - - - - - - 16 2222 (17) 0.63 0.08 0.03
BTB-01124458 13 6 683 656 - - - - - - 17 1430 (11) 0.62 0.07 0.04
1

Only the twenty most significant SNPs are shown.

2

SNPs identified commonly by both GenABEL and GenSel analyses; order is based on P-values from GenABEL.

3

SNPs identified only by GenABEL.

4

SNPs identified only by GenSel.

5

Bos Taurus chromosomes.

6

Position of SNP based on Bovine genome build UMD 3.1 (in base pair).

7

Major allele.

8

Minor allele.

9

Estimated effect of allele B (fitted allele) and the standard error of the estimated effect in the parenthesis.

10

P-value corrected by genomic control approach (GC).

11

Frequency of B allele in cases.

12

Frequency of B allele in controls.

13

Rank based on percentage of genetic variance among the twenty most significant windows by GenSel analysis.

14

Number of 1-Mb non-overlapping genome window and number of SNPs within each window in the parenthesis.

15

Percentage of total genetic variance explained by 1-Mb windows.

16

Proportion of models in which the corresponding window accounted for > 0.04% of genetic variance (expected variance if each window had the same effect: 1/total number of windows  = 2,657).

17

Proportion of MCMC iterations that included the corresponding SNP.