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 mr1115 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
vg0604357002 sf0604356003 6 4357002 1.85E-36 3.22E-16
vg0604350087 sf0604349088 6 4350087 1.91E-36 3.11E-16
vg0604336110 sf0604335111 6 4336110 3.53E-36 9.41E-16
vg0604208452 sf0604207453 6 4208452 4.89E-32 5.38E-14
vg1225206470 sf1225172868 12 25206470 3.38E-28 NA
vg0314622952 sf0314621639 3 14622952 7.78E-28 NA
vg0327376146 sf0327369199 3 27376146 7.85E-28 NA
vg1016611116 sf1016539889 10 16611116 1.04E-27 NA
vg0311384340 sf0311383058 3 11384340 2.71E-27 1.50E-06
vg0326986560 sf0326979613 3 26986560 7.08E-27 1.54E-06
vg1022854220 sf1022782693 10 22854220 5.71E-25 1.92E-06
vg0604160684 sf0604159685 6 4160684 1.43E-24 3.09E-09
vg0433048756 sf0432863643 4 33048756 2.85E-24 1.95E-06
vg0524319193 sf0524256612 5 24319193 2.19E-23 4.73E-06
vg0604237628 sf0604236629 6 4237628 NA 6.36E-12
vg0326933756 sf0326926809 3 26933756 NA 3.61E-09
vg0604184508 sf0604183509 6 4184508 NA 5.23E-09
vg0604726687 sf0604725688 6 4726687 NA 1.76E-07
vg0314888685 sf0314887332 3 14888685 NA 2.83E-07
vg0706319441 sf0706318444 7 6319441 NA 3.50E-07
vg0702783022 sf0702782023 7 2783022 NA 5.29E-07
vg1118412008 sf1117945868 11 18412008 NA 1.71E-06
vg1120916800 sf1120450703 11 20916800 NA 1.76E-06
vg1013275525 sf1013204295 10 13275525 NA 1.89E-06
vg0806234971 sf0806233976 8 6234971 NA 2.57E-06
vg1120091074 sf1119624997 11 20091074 NA 4.18E-06