Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1486 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg1001381044 sf1001380021 10 1381044 3.08E-24 3.89E-30
vg1001381368 sf1001380345 10 1381368 3.86E-24 5.23E-30
vg1001214204 sf1001213181 10 1214204 1.24E-22 8.56E-20
vg1001229450 sf1001228427 10 1229450 6.81E-21 2.14E-20
vg1001363789 sf1001362766 10 1363789 5.31E-20 1.12E-19
vg1001395791 sf1001394768 10 1395791 1.35E-15 2.84E-11
vg1001394803 sf1001393780 10 1394803 2.88E-15 3.83E-12
vg1001459935 sf1001458912 10 1459935 8.67E-15 3.23E-18
vg1001651113 sf1001650090 10 1651113 1.62E-13 2.00E-16
vg1001244483 sf1001243460 10 1244483 2.65E-12 1.19E-14
vg1001500421 sf1001499398 10 1500421 9.84E-12 7.85E-08
vg0107367191 sf0107366191 1 7367191 1.41E-07 9.35E-07
vg1001321073 sf1001320050 10 1321073 1.59E-07 4.35E-08
vg0529552096 sf0529489451 5 29552096 2.37E-07 1.76E-08
vg0412555488 sf0412546198 4 12555488 7.51E-07 5.81E-07
vg0726205357 sf0726204363 7 26205357 1.07E-06 8.06E-07
vg0720737728 sf0720736735 7 20737728 1.13E-06 9.81E-08
vg0702445862 sf0702444863 7 2445862 2.06E-06 2.11E-07
vg0300175534 sf0300174534 3 175534 2.49E-06 4.15E-07
vg1001434429 sf1001433406 10 1434429 3.36E-06 7.06E-11
vg0418111528 sf0417939571 4 18111528 4.38E-06 2.15E-07
vg0620356290 sf0620355293 6 20356290 5.42E-06 7.82E-07
vg1002107770 sf1002106747 10 2107770 NA 9.66E-10
vg1022763526 sf1022691999 10 22763526 NA 1.55E-07
vg0420807529 sf0420635572 4 20807529 NA 3.73E-07
vg0820948192 sf0820945479 8 20948192 NA 8.56E-07
vg0420802745 sf0420630788 4 20802745 NA 6.58E-06