From: Genome-wide association study of agronomic traits in rice cultivated in temperate regions
structure | PCA | ||||||||
---|---|---|---|---|---|---|---|---|---|
SNP | Loci number | Chr | Pos | p-value | q-values | % explained variance | p-value | q-values | % explained variance |
H-1 | 1 | 7 | 26,125,810 | 8.53E-04 | 0.691 | 5.5 | |||
H-2 | 2 | 8 | 26,290,663 | 5.74E-05 | 0.098 | 8.0 | 1.54E-05 | 0.026 | 9.0 |
DH-1 | 3 | 4 | 15,171,082 | 2.33E-06 | 0.002 | 14.3 | 1.01E-05 | 0.009 | 12.5 |
DH-2 | 4 | 5 | 13,373,075 | 2.76E-05 | 0.014 | 8.9 | 6.75E-05 | 0.031 | 8.1 |
DH-3 | 5 | 6 | 7,249,825 | 6.91E-07 | 0.001 | 12.4 | 1.67E-07 | 0.000 | 13.5 |
DH-4 | 6 | 6 | 8,122,336 | 1.82E-04 | 0.058 | 7.2 | 7.18E-05 | 0.031 | 8.0 |
DH-5 | 7 | 6 | 11,002,220 | 7.12E-04 | 0.185 | 7.4 | |||
DH-6 | 7 | 6 | 11,018,229 | 1.94E-04 | 0.058 | 7.1 | 9.60E-05 | 0.033 | 7.7 |
DH-7 | 8 | 10 | 1,366,920 | 9.09E-04 | 0.181 | 7.2 | |||
DH-8 | 8 | 10 | 1,500,932 | 3.10E-04 | 0.078 | 6.7 | |||
DH-9 | 8 | 10 | 1,871,964 | 7.59E-04 | 0.185 | 5.8 | |||
PL-1 | 9 | 1 | 6,126,957 | 7.34E-05 | 0.054 | 7.7 | |||
PL-2 | 10 | 2 | 35,406,962 | 6.78E-04 | 0.119 | 5.8 | |||
PL-3 | 11 | 3 | 1,003,670 | 3.09E-04 | 0.081 | 6.7 | 6.48E-04 | 0.119 | 5.9 |
PL-4 | 12 | 3 | 19,250,700 | 6.99E-04 | 0.119 | 7.2 | |||
PL-5 | 12 | 3 | 19,349,943 | 9.37E-04 | 0.169 | 8.1 | 5.93E-04 | 0.119 | 8.5 |
PL-6 | 13 | 3 | 29,987,079 | 2.49E-04 | 0.081 | 6.8 | 8.55E-04 | 0.131 | 5.5 |
PL-7 | 14 | 4 | 4,758,113 | 3.15E-04 | 0.081 | 6.6 | 1.98E-04 | 0.084 | 6.9 |
PL-8 | 15 | 5 | 20,125,768 | 6.72E-04 | 0.136 | 5.9 | |||
PL-9 | 15 | 5 | 21,838,857 | 3.52E-04 | 0.081 | 6.5 | |||
PL-10 | 16 | 5 | 28,626,704 | 1.21E-05 | 0.020 | 11.3 | 1.43E-05 | 0.024 | 10.8 |
PL-11 | 17 | 7 | 6,375,823 | 6.80E-05 | 0.055 | 9.7 | |||
PL-12 | 18 | 8 | 24,250,565 | 3.15E-04 | 0.108 | 8.0 | |||
PL-13 | 19 | 9 | 19,877,778 | 9.50E-05 | 0.054 | 7.5 | |||
PL-14 | 20 | 10 | 17,376,318 | 1.19E-04 | 0.064 | 9.2 | 4.78E-04 | 0.119 | 7.6 |
GN-1 | 21 | 1 | 38,011,958 | 4,33E-04 | 0,064 | 6,4 | |||
GN-2 | 21 | 1 | 40,012,174 | 5,64E-04 | 0,070 | 6,1 | |||
GN-3 | 22 | 2 | 2,720,687 | 2,99E-04 | 0,056 | 6,7 | |||
GN-4 | 22 | 2 | 3,755,851 | 1,89E-04 | 0,044 | 7,1 | |||
GN-5 | 23 | 2 | 32,500,801 | 3,46E-04 | 0,056 | 8,1 | |||
GN-6 | 23 | 2 | 34,386,360 | 3,25E-04 | 0,056 | 6,6 | |||
GN-7 | 24 | 3 | 17,999,538 | 1,39E-04 | 0,044 | 7,4 | |||
GN-8 | 25 | 3 | 18,500,293 | 3,23E-05 | 0,013 | 8,7 | 9,63E-04 | 0,197 | 5,2 |
GN-9 | 26 | 3 | 19,125,149 | 3,23E-05 | 0,013 | 8,7 | 9,63E-04 | 0,197 | 5,2 |
GN-10 | 27 | 3 | 20,500,343 | 3,23E-05 | 0,013 | 8,7 | 9,63E-04 | 0,197 | 5,2 |
GN-11 | 28 | 3 | 20,875,010 | 3,23E-05 | 0,013 | 8,7 | 9,63E-04 | 0,197 | 5,2 |
GN-12 | 28 | 5 | 2,460,569 | 7,67E-04 | 0,197 | 5,2 | |||
GN-13 | 28 | 5 | 2,753,203 | 1,48E-04 | 0,197 | 6,6 | |||
GN-14 | 29 | 5 | 6,499,710 | 9,98E-04 | 0,197 | 6,5 | |||
GN-15 | 30 | 9 | 9,375,311 | 5,58E-04 | 0,070 | 6,2 | 9,06E-04 | 0,197 | 5,4 |
GN-16 | 31 | 11 | 15,123,344 | 1,87E-04 | 0,044 | 7,2 | |||
PN-1 | 32 | 2 | 7,879,224 | 9.94E-04 | 0.710 | 5.5 | |||
PN-2 | 33 | 3 | 30,752,398 | 2.15E-04 | 0.318 | 6.9 | 1.20E-04 | 0.171 | 6.5 |