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 mr1191 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
vg1125545020 sf1125078859 11 25545020 3.03E-40 1.84E-29
vg1125897494 sf1125431413 11 25897494 3.17E-21 1.09E-18
vg1125148067 sf1124681907 11 25148067 8.29E-18 1.54E-14
vg0204430393 sf0204430390 2 4430393 3.71E-17 4.82E-13
vg0507714473 sf0507714414 5 7714473 1.74E-14 3.40E-10
vg1125798988 sf1125332909 11 25798988 3.92E-14 6.20E-12
vg0819689109 sf0819686396 8 19689109 6.40E-14 1.56E-08
vg1124998850 sf1124532690 11 24998850 5.39E-13 5.04E-10
vg1204309286 sf1204308274 12 4309286 9.93E-13 1.34E-08
vg0224605253 sf0224599384 2 24605253 1.32E-12 2.17E-12
vg1125216297 sf1124750137 11 25216297 1.43E-12 1.82E-08
vg1125465977 sf1124999816 11 25465977 1.84E-12 1.09E-09
vg1114596184 sf1114132502 11 14596184 6.78E-12 6.83E-08
vg1125964996 sf1125493410 11 25964996 1.87E-11 1.40E-10
vg1125602748 sf1125136587 11 25602748 5.26E-11 2.22E-14
vg1125569375 sf1125103214 11 25569375 8.76E-11 1.25E-10
vg0905257728 sf0905256728 9 5257728 8.94E-11 2.16E-08
vg1125391579 sf1124925418 11 25391579 1.04E-10 4.21E-08
vg1125862812 sf1125396731 11 25862812 1.07E-10 8.00E-10
vg0515506202 sf0515448743 5 15506202 6.79E-10 1.46E-08
vg1126338061 sf1125866474 11 26338061 7.41E-10 2.02E-08
vg0525036702 sf0524974117 5 25036702 4.49E-08 3.28E-08