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 mr1484 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
vg1125118463 sf1124652303 11 25118463 2.03E-54 1.39E-43
vg1125432386 sf1124966225 11 25432386 8.81E-25 7.45E-13
vg0704627367 sf0704626368 7 4627367 1.14E-22 5.51E-09
vg1125393828 sf1124927667 11 25393828 1.28E-22 5.02E-17
vg0124266409 sf0124265365 1 24266409 4.72E-22 7.45E-08
vg0619609667 sf0619608670 6 19609667 2.71E-21 5.87E-07
vg1125042652 sf1124576492 11 25042652 5.39E-21 3.65E-19
vg1124989620 sf1124523460 11 24989620 9.31E-21 6.57E-17
vg0124119893 sf0124118849 1 24119893 1.21E-19 7.52E-09
vg1124989458 sf1124523298 11 24989458 8.16E-19 8.17E-17
vg1124256871 sf1123790741 11 24256871 1.44E-18 9.80E-11
vg1124875808 sf1124409648 11 24875808 3.85E-17 1.50E-09
vg0814414168 sf0814411454 8 14414168 7.15E-17 NA
vg1125080303 sf1124614143 11 25080303 6.16E-16 3.89E-14
vg0134467592 sf0134466549 1 34467592 7.21E-16 1.31E-08
vg1125117525 sf1124651365 11 25117525 NA 1.47E-20
vg1125113390 sf1124647230 11 25113390 NA 2.74E-14
vg1125089512 sf1124623352 11 25089512 NA 5.85E-13
vg1124988847 sf1124522687 11 24988847 NA 1.76E-11
vg1125389716 sf1124923555 11 25389716 NA 2.84E-11
vg1125257504 sf1124791344 11 25257504 NA 8.54E-11
vg1124998698 sf1124532538 11 24998698 NA 2.20E-10
vg1125079888 sf1124613728 11 25079888 NA 2.28E-10
vg1125393643 sf1124927482 11 25393643 NA 1.33E-09
vg1125238334 sf1124772174 11 25238334 NA 1.45E-09
vg0704635310 sf0704634311 7 4635310 NA 2.60E-09
vg0617714131 sf0617713134 6 17714131 NA 1.55E-08