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 mr1057 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
vg0105145738 sf0105144738 1 5145738 4.83E-41 1.35E-36
vg0207368924 sf0207368924 2 7368924 2.55E-19 5.62E-11
vg0723101562 sf0723100569 7 23101562 7.04E-19 2.02E-08
vg0105134457 sf0105133457 1 5134457 4.86E-16 3.88E-11
vg0919071881 sf0919071470 9 19071881 3.67E-15 4.52E-08
vg0207379019 sf0207379019 2 7379019 3.89E-15 7.84E-13
vg1221673234 sf1221639781 12 21673234 1.07E-14 1.92E-08
vg0623064422 sf0623063425 6 23064422 9.32E-11 1.56E-08
vg0709781857 sf0709780863 7 9781857 2.46E-10 2.83E-08
vg0810013102 sf0810012106 8 10013102 4.08E-10 1.68E-09
vg0810145472 sf0810144476 8 10145472 1.17E-09 5.41E-10
vg0105181705 sf0105180705 1 5181705 3.68E-08 3.50E-08
vg0335950921 sf0335943790 3 35950921 1.08E-07 4.20E-10
vg1221003277 sf1220969827 12 21003277 2.16E-07 2.88E-08
vg1122439094 sf1121972965 11 22439094 2.37E-07 4.03E-08
vg0105163864 sf0105162864 1 5163864 5.08E-07 4.63E-25
vg0524064354 sf0524001774 5 24064354 NA 6.09E-09
vg1221582274 sf1221548821 12 21582274 NA 6.29E-09
vg0207368784 sf0207368784 2 7368784 NA 3.20E-08
vg0722882681 sf0722881688 7 22882681 NA 3.95E-08
vg1020380304 sf1020308784 10 20380304 NA 4.28E-08
vg0126772523 sf0126771479 1 26772523 NA 1.05E-07
vg0416374336 sf0416202374 4 16374336 NA 9.43E-06