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 mr1402 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
vg0406465683 sf0406461126 4 6465683 1.99E-21 9.87E-17
vg0503312521 sf0503312497 5 3312521 1.87E-10 2.86E-07
vg0807357132 sf0807356137 8 7357132 6.58E-09 5.22E-07
vg0900561007 sf0900560007 9 561007 1.32E-08 NA
vg0405063978 sf0405059417 4 5063978 2.02E-08 NA
vg0809703428 sf0809702432 8 9703428 2.74E-08 5.80E-07
vg1209797289 sf1209794699 12 9797289 4.33E-08 2.78E-07
vg0406056639 sf0406052078 4 6056639 6.52E-08 4.01E-07
vg0700974440 sf0700973440 7 974440 1.59E-07 3.96E-06
vg1123406801 sf1122940671 11 23406801 1.32E-06 NA
vg1116610872 sf1116145750 11 16610872 1.32E-06 4.00E-06
vg0707039898 sf0707038903 7 7039898 3.06E-06 4.32E-06
vg0628039466 sf0628038468 6 28039466 NA 1.99E-06