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 mr1251 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
vg0217071444 sf0217065574 2 17071444 2.50E-35 7.86E-23
vg0900337327 sf0900336327 9 337327 1.13E-17 1.11E-10
vg0213525745 sf0213525741 2 13525745 4.22E-16 6.74E-07
vg1114870126 sf1114406440 11 14870126 2.53E-13 5.40E-09
vg1114596727 sf1114133045 11 14596727 2.81E-13 NA
vg0217677364 sf0217671494 2 17677364 6.68E-13 1.90E-08
vg1005364262 sf1005380799 10 5364262 1.06E-12 2.77E-08
vg0631235279 sf0631234281 6 31235279 2.62E-12 3.40E-06
vg1114473442 sf1114009759 11 14473442 4.26E-11 1.97E-06
vg0908235271 sf0908234271 9 8235271 6.31E-11 6.55E-07
vg0216616442 sf0216610572 2 16616442 4.25E-10 1.89E-07
vg0217377961 sf0217372091 2 17377961 5.09E-10 4.22E-06
vg0217737606 sf0217731736 2 17737606 8.15E-10 3.05E-06
vg0404017804 sf0404013411 4 4017804 3.85E-08 1.33E-06
vg1112889066 sf1112425387 11 12889066 1.25E-07 8.40E-07
vg0404020437 sf0404016044 4 4020437 2.00E-07 1.95E-06
vg0607317396 sf0607316397 6 7317396 NA 3.86E-06