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 mr1334 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
vg1220025663 sf1219997105 12 20025663 8.47E-49 4.53E-25
vg1220023929 sf1219995371 12 20023929 5.96E-48 3.05E-25
vg1224806805 sf1224773259 12 24806805 9.52E-27 2.25E-10
vg1216132870 sf1216130166 12 16132870 3.34E-22 1.29E-06
vg0216564333 sf0216558463 2 16564333 2.16E-21 NA
vg0114831954 sf0114830928 1 14831954 1.12E-20 NA
vg1220129699 sf1220101141 12 20129699 NA 4.53E-07
vg0226125680 sf0226119811 2 26125680 NA 9.83E-07
vg0804876696 sf0804875699 8 4876696 NA 9.97E-07
vg0807357132 sf0807356137 8 7357132 NA 1.24E-06
vg1119557203 sf1119090891 11 19557203 NA 1.48E-06
vg1219857888 sf1219829358 12 19857888 NA 1.64E-06