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 mr1371 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
vg0607692076 sf0607691077 6 7692076 2.04E-09 9.01E-07
vg0904348676 sf0904347676 9 4348676 7.58E-09 NA
vg0232208358 sf0232202489 2 32208358 8.22E-09 4.52E-06
vg0907521059 sf0907520059 9 7521059 9.48E-09 NA
vg0210303462 sf0210303460 2 10303462 5.52E-08 7.74E-06
vg0232481318 sf0232475449 2 32481318 8.35E-08 6.51E-07
vg1209946610 sf1209944020 12 9946610 9.55E-08 3.17E-06
vg0419828219 sf0419656256 4 19828219 1.63E-06 4.59E-06
vg0608550861 sf0608549862 6 8550861 4.30E-06 2.46E-07
vg0610412240 sf0610411241 6 10412240 5.46E-06 4.19E-06
vg0431043984 sf0430858869 4 31043984 NA 7.53E-07
vg0819150140 sf0819147427 8 19150140 NA 3.05E-06
vg1112967711 sf1112504032 11 12967711 NA 3.77E-06
vg0227578016 sf0227572147 2 27578016 NA 4.08E-06
vg0510460804 sf0510460733 5 10460804 NA 4.63E-06
vg0707836859 sf0707835864 7 7836859 NA 4.68E-06