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 mr1009 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
vg0133471381 sf0133470337 1 33471381 5.04E-175 1.36E-39
vg0133489903 sf0133488859 1 33489903 1.05E-172 8.08E-40
vg0130140335 sf0130139290 1 30140335 5.86E-128 4.34E-07
vg0130725638 sf0130724594 1 30725638 6.53E-120 5.56E-09
vg0903208447 sf0903207447 9 3208447 2.00E-118 2.58E-06
vg0900651975 sf0900650975 9 651975 2.28E-116 NA
vg0137243519 sf0137242476 1 37243519 4.98E-115 NA
vg0920477382 sf0920476901 9 20477382 6.21E-112 8.95E-07
vg0901044144 sf0901043144 9 1044144 3.76E-107 3.64E-10
vg1015248198 sf1015176966 10 15248198 1.01E-103 1.99E-06
vg0331909359 sf0331902236 3 31909359 4.53E-103 1.42E-06
vg0133259170 sf0133258126 1 33259170 NA 6.02E-08
vg0133276859 sf0133275815 1 33276859 NA 1.12E-07
vg0133479485 sf0133478441 1 33479485 NA 1.34E-07
vg0118219073 sf0118218027 1 18219073 NA 1.05E-06
vg1015840569 sf1015769339 10 15840569 NA 1.39E-06
vg0135170016 sf0135168973 1 35170016 NA 2.92E-06
vg0434702618 sf0434517507 4 34702618 NA 3.04E-06
vg0140894558 sf0140893515 1 40894558 NA 3.23E-06
vg0529102043 sf0529039398 5 29102043 NA 3.34E-06
vg0907602051 sf0907601051 9 7602051 NA 3.85E-06
vg0917927607 sf0917926606 9 17927607 NA 4.29E-06