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 mr1902 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
vg0331273085 sf0331265970 3 31273085 1.14E-32 4.46E-14
vg0331220415 sf0331213300 3 31220415 2.43E-32 4.28E-15
vg0205108560 sf0205108557 2 5108560 7.20E-18 7.55E-06
vg1103577713 sf1103573616 11 3577713 1.74E-14 NA
vg0424051857 sf0423866718 4 24051857 2.15E-14 NA
vg1117845191 sf1117379047 11 17845191 2.55E-14 NA
vg0331795700 sf0331788577 3 31795700 4.55E-13 3.89E-07
vg1020877689 sf1020806168 10 20877689 2.24E-11 1.14E-06
vg0205036609 sf0205036606 2 5036609 3.85E-11 5.05E-07
vg0712969979 sf0712968986 7 12969979 NA 2.05E-06
vg0421298734 sf0421126788 4 21298734 NA 2.22E-06
vg0508574937 sf0508574865 5 8574937 NA 2.71E-06
vg0623683404 sf0623682407 6 23683404 NA 3.57E-06
vg0335143934 sf0335136804 3 35143934 NA 4.57E-06
vg1121848527 sf1121382404 11 21848527 NA 4.87E-06