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 mr1121 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
vg0610567538 sf0610566539 6 10567538 1.24E-103 1.21E-34
vg0610567030 sf0610566031 6 10567030 1.53E-103 1.39E-34
vg0610645257 sf0610644258 6 10645257 1.03E-79 5.65E-23
vg0312570316 sf0312569034 3 12570316 1.28E-55 NA
vg0715304997 sf0715304004 7 15304997 4.14E-55 NA
vg0501552250 sf0501552234 5 1552250 1.27E-54 NA
vg0435357013 sf0435171895 4 35357013 2.50E-54 NA
vg0610539571 sf0610538572 6 10539571 NA 2.42E-15
vg0610763769 sf0610762770 6 10763769 NA 2.42E-12
vg0610720006 sf0610719007 6 10720006 NA 5.84E-10
vg0615907055 sf0615906057 6 15907055 NA 1.37E-09
vg0611127099 sf0611126100 6 11127099 NA 2.43E-09
vg0609930953 sf0609929954 6 9930953 NA 3.98E-09
vg0618930430 sf0618929433 6 18930430 NA 1.95E-08
vg0410126589 sf0410117286 4 10126589 NA 4.70E-08
vg0617631923 sf0617630926 6 17631923 NA 7.47E-08
vg0613067756 sf0613066757 6 13067756 NA 1.87E-07
vg0610679715 sf0610678716 6 10679715 NA 3.05E-07
vg0606968664 sf0606967665 6 6968664 NA 4.53E-07
vg0613339384 sf0613338385 6 13339384 NA 7.70E-07
vg0617636590 sf0617635593 6 17636590 NA 9.32E-07
vg0122725848 sf0122724804 1 22725848 NA 1.10E-06
vg0610442214 sf0610441215 6 10442214 NA 1.14E-06
vg0612255863 sf0612254864 6 12255863 NA 1.21E-06
vg0611906755 sf0611905756 6 11906755 NA 1.29E-06
vg0139981469 sf0139980426 1 39981469 NA 1.29E-06
vg0610105888 sf0610104889 6 10105888 NA 1.72E-06