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 mr1063 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
vg1010655735 sf1010584556 10 10655735 5.69E-62 NA
vg0718989677 sf0718988684 7 18989677 4.09E-60 NA
vg0302691320 sf0302690316 3 2691320 6.05E-60 NA
vg0229733566 sf0229727697 2 29733566 1.27E-59 NA
vg0233946459 sf0233940590 2 33946459 5.74E-59 NA
vg0326857364 sf0326850417 3 26857364 8.46E-53 NA
vg0222739831 sf0222733962 2 22739831 NA 3.95E-13
vg0222746228 sf0222740359 2 22746228 NA 4.30E-09
vg0315803692 sf0315802339 3 15803692 NA 2.30E-06
vg0724379241 sf0724378247 7 24379241 NA 2.85E-06
vg1101271092 sf1101270093 11 1271092 NA 7.15E-06
vg0621194085 sf0621193088 6 21194085 NA 8.35E-06