Table 2.
LG | Pos | SNP | Test | N | Effect | Stat | P-value | Sig | GeneID |
---|---|---|---|---|---|---|---|---|---|
1 | 60.3 | 39454_862 | GRAMMAS | 1007 | 1.14(0.53) | 4.66 | 0.0032 | unknown | |
2 | 0 | 47460_2015 | QFAM | 1024 | -4.538 | 56.81 | 0.0094 | dna p58 subunit | |
2 | 21.6 | 52022_4578 | QFAM | 1020 | 6.351 | 83.1 | 0.0049 | plasminogen activator inhibitor 1 rna-binding protein | |
2 | 24.5 | 50149_330 | FASTA | 983 | 3.32(1.03) | 10.49 | 0.0014 | thyroid transcription factor 1-associated protein 26-like protein | |
2 | 24.5 | 50149_330 | GRAMMAS | 983 | 1.65(0.71) | 5.44 | 0.0015 | thyroid transcription factor 1-associated protein 26-like protein | |
2 | 30.5 | 52064_948 | GRAMMAS | 1007 | 0.95(0.49) | 3.79 | 0.008 | polymerase I polypeptide 194kda | |
2 | 36.6 | 36607_579 | GRAMMAS | 1006 | -0.91(0.46) | 3.94 | 0.0068 | unknown | |
2 | 53.5 | 28698_101 | GRAMMAS | 965 | -1.01(0.48) | 4.4 | 0.0042 | unknown | |
2 | 53.5 | 28698_101 | FASTA | 965 | -1.75(0.65) | 7.22 | 0.0082 | unknown | |
2 | 61.8 | 51997_2402 | QFAM | 1023 | -5.49 | 139.2 | 0.0009 | * | runt protein 1a |
2 | 62.5 | 35650_1855 | FASTA | 1004 | 2.11(0.79) | 7.23 | 0.0081 | unknown | |
2 | 62.5 | 35650_1855 | QFAM | 1018 | 5.408 | 100.5 | 0.0085 | unknown | |
3 | 14.6 | 38676_1386 | QFAM | 1021 | -4.2 | 41.79 | 0.0069 | actin-binding rho-activating | |
3 | 29.5 | 41442_2163 | GRAMMAS | 1006 | -1.35(0.55) | 5.99 | 0.0008 | * | flagellar hook-length control protein flik |
3 | 29.5 | 41442_2163 | FASTA | 1006 | -1.88(0.68) | 7.62 | 0.0066 | flagellar hook-length control protein flik | |
5 | 21.2 | 45605_1545 | FASTA | 1007 | 7.34(1.94) | 14.26 | 0.0002 | * | ubiquitin domain-containing protein ubfd1 |
5 | 21.2 | 45605_1545 | GRAMMAS | 1007 | 2.42(1.06) | 5.22 | 0.0018 | ubiquitin domain-containing protein ubfd1 | |
5 | 21.9 | 35133_160 | FASTA | 991 | -2.98(0.96) | 9.56 | 0.0023 | unknown | |
5 | 21.9 | 35133_160 | GRAMMAS | 991 | -1.42(0.65) | 4.81 | 0.0028 | unknown | |
5 | 22.3 | 44076_3116 | GRAMMAS | 1004 | -1.15(0.49) | 5.4 | 0.0015 | vacuolar proton atpase | |
5 | 22.3 | 44076_3116 | FASTA | 1004 | -1.82(0.65) | 7.79 | 0.006 | vacuolar proton atpase | |
5 | 87 | 45237_316 | GridQTL | 1024 | 11.96(2.44) | 24 | 0.0048 | * | |
5 | 96.5 | 30527_111 | FASTA | 992 | -1.88(0.68) | 7.67 | 0.0064 | unknown | |
6 | 17.3 | 29124_228 | FASTA | 1007 | 4.82(1.34) | 12.88 | 0.0004 | * | paired-like homeodomain transcription factor 3 |
6 | 17.3 | 29124_228 | GRAMMAS | 1007 | 1.49(0.71) | 4.42 | 0.0042 | paired-like homeodomain transcription factor 3 | |
6 | 39 | 50756_3741–46539_1081 | GridQTL | 1024 | 11.25(2.32) | 23.54 | 0.0098 | * | |
6 | 42.8 | 33044_1018 | FASTA | 1007 | 3.65(1.15) | 10.07 | 0.0018 | erythrocyte band 7 integral membrane protein | |
8 | 45.4 | 52776_1335 | QFAM | 1021 | 5.849 | 56.79 | 0.0036 | abb73282reverse transcriptase | |
9 | 10.4 | 42679_345 | QFAM | 1007 | 4.823 | 81.8 | 0.0039 | unknown | |
9 | 59.9 | 48064_77 | QFAM | 1024 | 4.807 | 126.6 | 0.0072 | unknown | |
11 | 24.7 | 60951_72 | FASTA | 1007 | -3.46(1.14) | 9.2 | 0.0028 | unknown | |
11 | 24.7 | 60951_72 | GRAMMAS | 1007 | -1.37(0.68) | 4.05 | 0.0061 | unknown | |
11 | 38.1 | 46551_1072 | QFAM | 1024 | 5.642 | 135.6 | 0.0016 | multidrug resistance-associated protein 14 | |
11 | 59.4 | 23272_344 | FASTA | 1007 | 3.52(1.33) | 7.01 | 0.0091 | 26 s protease regulatory subunit | |
13 | 18 | 29098_2532 | QFAM | 1024 | 3.95 | 50.35 | 0.0076 | actin-binding homolog 1 | |
14 | 49.5 | 40042_2041 | QFAM | 1021 | 4.192 | 46.08 | 0.0046 | unknown | |
15 | 27.2 | 32667_1134 | QFAM | 1023 | -5.196 | 104.9 | 0.0067 | usick-kaufman syndrome | |
15 | 47.8 | 44399_644 | FASTA | 1007 | 2.28(0.78) | 8.61 | 0.0039 | unknown | |
16 | 11 | 42291_720 | GRAMMAS | 1007 | 2.13(0.93) | 5.24 | 0.0018 | adp-ribosylation factor-like 2 binding protein | |
16 | 11 | 42291_720 | FASTA | 1007 | 4(1.34) | 8.91 | 0.0033 | adp-ribosylation factor-like 2 binding protein | |
16 | 11 | 38195_1528 | FASTA | 1003 | 2.46(0.84) | 8.52 | 0.0041 | fanconi anemia group a protein homolog | |
16 | 23.4 | 45647_100 | QFAM | 1018 | -4.662 | 56.63 | 0.009 | glutamyl-trna amidotransferase subunit | |
16 | 38.1 | 35920_135 | QFAM | 1012 | 3.142 | 43.9 | 0.0018 | unknown | |
16 | 39.2 | 5999_123 | QFAM | 1024 | 6.677 | 92.39 | 0.0049 | unknown | |
17 | 8.3 | 39727_708 | GRAMMAS | 1007 | 0.82(0.41) | 4.01 | 0.0063 | unknown | |
17 | 26.7 | 26178_2213 | QFAM | 1018 | -4.67 | 78.32 | 0.0067 | bobby sox | |
17 | 29 | 47941_2759 | FASTA | 1007 | 2.75(1.01) | 7.34 | 0.0076 | alsin isoform 2 | |
17 | 54 | 25133_74 to 36717_243 | GridQTL | 1024 | 22.90 (2.42) | 89.81 | 0.0001 | ** | |
18 | 15.1 | 44821_270 | FASTA | 1006 | 7.26(1.85) | 15.34 | 0.0001 | ** | unknown |
18 | 15.1 | 44821_270 | GRAMMAS | 1006 | 3.35(1.2) | 7.83 | 0.0001 | ** | unknown |
18 | 81.5 | 24411_90 | GRAMMAS | 1006 | -0.9(0.46) | 3.83 | 0.0076 | unknown | |
19 | 34.8 | 35006_276 | QFAM | 1024 | 5.931 | 92.83 | 0.0011 | alanyl-trna synthetase | |
19 | 44.5 | 14555_138 | QFAM | 1021 | 6.616 | 125.5 | 0.006 | unknown | |
19 | 70.9 | 51029_2543 | QFAM | 1023 | -3.578 | 40.82 | 0.0029 | insulin receptor substrate 1 | |
19 | 82.4 | 50096_1789 | QFAM | 1021 | 5.243 | 77.12 | 0.0005 | * | ankyrin repeat |
20 | 23.1 | 36484_493 | FASTA | 1007 | 3.48(1.31) | 7.01 | 0.0091 | mitochondrial ribosomal protein l2 | |
20 | 63.1 | 42447_399 | GRAMMAS | 1007 | -1.14(0.57) | 4.04 | 0.0062 | unknown | |
20 | 63.1 | 42447_399 | FASTA | 1007 | -2.26(0.84) | 7.26 | 0.008 | unknown | |
21 | 20.1 | 47262_891 | GRAMMAS | 1007 | -0.93(0.45) | 4.19 | 0.0053 | myostatin 1b | |
21 | 20.1 | 47262_891 | FASTA | 1007 | -1.75(0.66) | 7.17 | 0.0084 | myostatin 1b | |
21 | 20.1 | 47262_891 | QFAM | 1024 | -4.787 | 82.96 | 0.0017 | myostatin 1b | |
21 | 26 | 30265_1829 | FASTA | 1007 | 1.96(0.68) | 8.44 | 0.0042 | unknown | |
21 | 26 | 30265_1829 | GRAMMAS | 1007 | 0.88(0.43) | 4.2 | 0.0052 | unknown | |
21 | 28.5 | 29404_373 | GRAMMAS | 1007 | 1.26(0.63) | 4.05 | 0.0061 | unknown | |
21 | 28.8 | 19638_158 | QFAM | 1011 | 4.032 | 45.59 | 0.008 | unknown | |
21 | 89.5 | 40988_772 | GRAMMAS | 1007 | -0.98(0.5) | 3.77 | 0.0082 | c12orf66-like | |
22 | 9.1 | 52229_3858 | GRAMMAS | 1003 | -1.08(0.55) | 3.8 | 0.0079 | nucleolar pre-ribosomal-associated protein 1-like | |
22 | 20.8 | 25410_46 | GRAMMAS | 986 | -1.13(0.51) | 4.96 | 0.0024 | unknown | |
22 | 27.9 | 18472_352 | FASTA | 1007 | -2.11(0.76) | 7.69 | 0.0063 | unknown | |
22 | 27.9 | 18472_352 | GRAMMAS | 1007 | -0.98(0.49) | 3.97 | 0.0066 | unknown | |
22 | 27.9 | 18472_352 | QFAM | 1024 | -5.815 | 104.9 | 0.0001 | ** | unknown |
23 | 83.5 | 41044_732 | QFAM | 1024 | 5.885 | 110.7 | 0.0043 | unknown | |
24 | 0.4 | 49156_279 | GRAMMAS | 1007 | 1.11(0.55) | 4.13 | 0.0056 | haspin | |
24 | 0.4 | 49156_279 | FASTA | 1007 | 2.21(0.81) | 7.43 | 0.0073 | haspin | |
24 | 50.3 | 51251_2007 | QFAM | 1018 | -5.541 | 141.1 | 0.0023 | cub-serine protease | |
25 | 0 | 44977_264 | QFAM | 1024 | 4.927 | 61.93 | 0.004 | unknown | |
26 | 0.6 | 52048_2568 | GRAMMAS | 992 | -1.12(0.57) | 3.8 | 0.0079 | adenosine monophosphate-protein transferase ficd homolog | |
26 | 0.6 | 52048_2568 | QFAM | 1009 | -6.31 | 89.68 | 0.002 | adenosine monophosphate-protein transferase ficd homolog | |
26 | 8.5 | 44451_587 | QFAM | 1023 | 5.597 | 76.98 | 0.0021 | unknown | |
26 | 58.9 | 33059_367 | QFAM | 1024 | -5.422 | 69.94 | 0.0059 | unknown | |
27 | 40 | 18687_338-33729_523 | GridQTL | 1024 | 8.64(2.39) | 13.04 | 0.018 | * | |
27 | 52.7 | 47625_1438 | GRAMMAS | 1006 | -0.99(0.52) | 3.7 | 0.0087 | unknown | |
27 | 63.6 | 33004_1869 | GRAMMAS | 1007 | -1.26(0.59) | 4.51 | 0.0038 | unknown | |
27 | 91.9 | 43302_1775 | FASTA | 1007 | 2.2(0.8) | 7.54 | 0.0069 | dead box atp-dependent rna helicase | |
27 | 91.9 | 43302_1775 | GRAMMAS | 1007 | 0.98(0.51) | 3.73 | 0.0085 | dead box atp-dependent rna helicase | |
27 | 101.7 | 49263_1068 | GRAMMAS | 1007 | 1.67(0.77) | 4.73 | 0.003 | unknown | |
27 | 101.7 | 49263_1068 | FASTA | 1007 | 3.12(1.11) | 7.94 | 0.0055 | unknown | |
28 | 20.8 | 51400_2931 | GRAMMAS | 1006 | 1.32(0.63) | 4.38 | 0.0043 | unknown | |
28 | 20.8 | 51400_2931 | QFAM | 1019 | 4.917 | 43.37 | 0.0089 | unknown | |
28 | 30.6 | 47112_509 | FASTA | 1006 | -2.82(0.87) | 10.63 | 0.0013 | chorion peroxidase | |
29 | 29.7 | 52042_128 | QFAM | 1022 | 4.654 | 94.7 | 0.0065 | multiple c2 domain and transmembrane region | |
29 | 44 | 43412_2186 | GRAMMAS | 1007 | -1.35(0.71) | 3.58 | 0.0099 | gpi-anchor transamidase | |
29 | 53.7 | 32409_114 | FASTA | 1005 | 1.86(0.71) | 6.92 | 0.0096 | unknown | |
30 | 77.3 | 51299_1729 | QFAM | 1016 | 4.115 | 60.01 | 0.0047 | breast carcinoma-amplified sequence 3 homolog isoform 1 | |
31 | 14.7 | 36096_367 | FASTA | 1007 | 3.82(1.24) | 9.49 | 0.0024 | nucleostemin-like protein | |
32 | 36.6 | 47777_1061 | FASTA | 1002 | -1.82(0.7) | 6.85 | 0.01 | exonuclease 3–5 domain-containing protein 2 isoform 1 | |
32 | 36.6 | 47777_1061 | QFAM | 1012 | -4.716 | 76.83 | 0.0035 | exonuclease 3–5 domain-containing protein 2 isoform 1 | |
34 | 32.3 | 24101_537 | GRAMMAS | 1007 | -1.56(0.72) | 4.67 | 0.0032 | zinc finger protein 64-like | |
34 | 32.3 | 24101_537 | FASTA | 1007 | -2.68(0.99) | 7.25 | 0.008 | zinc finger protein 64-like | |
36 | 29.6 | 30057_491 | QFAM | 1023 | -5.252 | 75.55 | 0.009 | unknown | |
36 | 32.1 | 49829_3826 | QFAM | 962 | -4.221 | 71.99 | 0.0044 | unknown | |
36 | 57.6 | 50839_3313 | GRAMMAS | 1007 | 1.72(0.81) | 4.54 | 0.0037 | transcriptional enhancer factor tef- | |
36 | 57.6 | 50839_3313 | FASTA | 1007 | 3.08(1.14) | 7.33 | 0.0077 | transcriptional enhancer factor tef- | |
38 | 36.1 | 35013_386 | FASTA | 1007 | -2.31(0.72) | 10.32 | 0.0016 | unknown | |
38 | 36.1 | 35013_386 | GRAMMAS | 1007 | -0.88(0.42) | 4.36 | 0.0044 | unknown | |
38 | 66.9 | 17589_451 | GRAMMAS | 1004 | 1.67(0.82) | 4.12 | 0.0056 | unknown | |
39 | 0.2 | 35101_271 | QFAM | 1021 | 4.295 | 57.77 | 0.0045 | unknown | |
39 | 51.2 | 49386_1117 | QFAM | 1024 | -5.859 | 109.8 | 0.0086 | phospholipase c gamma | |
39 | 59.4 | 36972_442 | FASTA | 1004 | -1.85(0.66) | 7.82 | 0.0059 | unknown | |
39 | 59.4 | 36972_442 | GRAMMAS | 1004 | -0.83(0.42) | 3.86 | 0.0074 | unknown | |
40 | 22.9 | 51885_4402 | QFAM | 1024 | 5.687 | 50.84 | 0.007 | chromodomain-helicase-dna-binding protein 1 | |
40 | 68.1 | 11637_107 | QFAM | 1020 | -7.046 | 129.7 | 0.0083 | non-lysosomal glucosylceramidase | |
41 | 1.6 | 26900_757 | QFAM | 1021 | -7.651 | 113.7 | 0.0079 | unknown | |
42 | 59 | 35645_15 | GRAMMAS | 1005 | 0.99(0.46) | 4.73 | 0.003 | unknown | |
43 | 0.4 | 27976_64 | GRAMMAS | 990 | -1.4(0.52) | 7.3 | 0.0002 | * | unknown |
43 | 0.4 | 27976_64 | FASTA | 990 | -1.84(0.64) | 8.39 | 0.0044 | unknown | |
44 | 0 | 38601_555 | FASTA | 1007 | -2.39(0.88) | 7.41 | 0.0074 | unknown | |
44 | 0 | 38601_555 | GRAMMAS | 1007 | -1.1(0.57) | 3.77 | 0.0081 | unknown | |
44 | 3.2 | 42369_480 | QFAM | 1024 | -5.011 | 91.99 | 0.0058 | tbc1 domain family member 14 isoform a | |
44 | 26 | 51212_1738 | QFAM | 1024 | 6.066 | 107 | 0.0063 | sodium bicarbonate transporter-like protein 11 | |
44 | 40.4 | 20208_30 | GRAMMAS | 1007 | 1.55(0.79) | 3.8 | 0.0078 | unknown |
LG, linkage group; Pos, location on LG in centimorgans; N, number of progeny and parents analysed; Effect, allele substitution effect of the minor allele with standard error in parenthesis (FASTA, GRAMMAS and GridQTL), Beta (QFAM); Stat, test statistic linear regression coefficient for QFAM, chi-square with one degree of freedom for FASTA and GRAMMAS analyses, F-statistic for GridQTL; P, point-wise empirical P-value (QFAM), permuted P-value with one degree of freedom corrected for inflation factor lambda (FASTA and GRAMMAS) or chromosome-wide P search with permutation and bootstrap analysis (GridQTL); Sig, significance after Bonferroni correction (*P < 0.05; **P < 0.01). GeneID, closest SNP homology from BLAST. Tests were considered suggestive when P < 0.01 before Bonferroni correction.