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 mr1100 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
vg0222746228 sf0222740359 2 22746228 3.20E-22 1.31E-14
vg0406995300 sf0406990571 4 6995300 4.76E-13 1.29E-07
vg0618618072 sf0618617075 6 18618072 1.03E-12 6.32E-11
vg0406286994 sf0406282434 4 6286994 4.86E-12 NA
vg0120457652 sf0120456607 1 20457652 6.29E-12 NA
vg0406944478 sf0406939746 4 6944478 3.07E-10 3.09E-07
vg0224592985 sf0224587116 2 24592985 7.79E-10 1.36E-07
vg0222852279 sf0222846410 2 22852279 3.00E-09 4.35E-09
vg0224639472 sf0224633603 2 24639472 4.25E-09 2.32E-06
vg0613439992 sf0613438993 6 13439992 4.27E-09 6.04E-07
vg0424423524 sf0424238385 4 24423524 5.93E-09 4.58E-07
vg0920091049 sf0920090568 9 20091049 8.84E-08 1.62E-06
vg0222556850 sf0222550981 2 22556850 NA 1.32E-07
vg1225855934 sf1225822329 12 25855934 NA 1.60E-07
vg1216930362 sf1216924316 12 16930362 NA 4.91E-07
vg0412137273 sf0412127984 4 12137273 NA 7.52E-07
vg0606957055 sf0606956056 6 6957055 NA 9.82E-07
vg0618997817 sf0618996820 6 18997817 NA 1.01E-06
vg0514401778 sf0514344321 5 14401778 NA 1.26E-06
vg1215976459 sf1215973755 12 15976459 NA 1.31E-06
vg0806502338 sf0806501343 8 6502338 NA 1.76E-06
vg0621203049 sf0621202052 6 21203049 NA 2.46E-06
vg0618224048 sf0618223051 6 18224048 NA 3.00E-06
vg0616244147 sf0616243149 6 16244147 NA 3.41E-06