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 mr1008 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 1.88E-179 6.85E-41
vg0133489903 sf0133488859 1 33489903 3.19E-177 2.05E-41
vg0133438339 sf0133437295 1 33438339 1.88E-173 5.67E-36
vg0130140335 sf0130139290 1 30140335 8.30E-129 1.84E-06
vg0130725638 sf0130724594 1 30725638 3.81E-121 8.18E-09
vg0903208447 sf0903207447 9 3208447 3.94E-120 3.61E-06
vg0326760318 sf0326753372 3 26760318 1.15E-117 NA
vg0900651975 sf0900650975 9 651975 1.16E-117 NA
vg0920477382 sf0920476901 9 20477382 2.82E-114 1.37E-06
vg0901048364 sf0901047364 9 1048364 1.95E-109 2.75E-09
vg0133497043 sf0133495999 1 33497043 NA 4.43E-08
vg0133259170 sf0133258126 1 33259170 NA 9.32E-08
vg0133479485 sf0133478441 1 33479485 NA 3.94E-07
vg0140894558 sf0140893515 1 40894558 NA 7.94E-07
vg0907602051 sf0907601051 9 7602051 NA 1.95E-06
vg1015840569 sf1015769339 10 15840569 NA 2.23E-06
vg0118216631 sf0118215585 1 18216631 NA 2.24E-06
vg0135170016 sf0135168973 1 35170016 NA 3.39E-06