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 mr1123 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
vg0222725905 sf0222720036 2 22725905 1.90E-24 3.58E-17
vg0222726986 sf0222721117 2 22726986 5.49E-16 1.19E-10
vg0222726751 sf0222720882 2 22726751 2.20E-14 2.82E-09
vg1009142714 sf1009071575 10 9142714 2.59E-11 NA
vg0221968611 sf0221962742 2 21968611 3.92E-10 1.61E-07
vg0224284988 sf0224279119 2 24284988 1.15E-09 NA
vg0230005440 sf0229999571 2 30005440 7.80E-09 NA
vg0221953494 sf0221947625 2 21953494 8.40E-09 3.78E-07
vg0220941661 sf0220935793 2 20941661 2.06E-07 2.41E-06
vg0225037452 sf0225031583 2 25037452 4.23E-07 2.74E-08
vg0813652494 sf0813649779 8 13652494 4.73E-07 NA
vg0222271516 sf0222265647 2 22271516 1.00E-06 7.05E-08
vg0224748988 sf0224743119 2 24748988 NA 1.01E-07
vg0335379790 sf0335372659 3 35379790 NA 1.94E-07
vg0500262933 sf0500262933 5 262933 NA 2.71E-07
vg0920451675 sf0920451194 9 20451675 NA 2.71E-07
vg0525827641 sf0525765062 5 25827641 NA 3.53E-07
vg0225005075 sf0224999206 2 25005075 NA 8.65E-07
vg1128960749 sf1128437528 11 28960749 NA 1.13E-06
vg0139807295 sf0139806252 1 39807295 NA 1.66E-06
vg0504390095 sf0504390072 5 4390095 NA 2.61E-06
vg0224480548 sf0224474679 2 24480548 NA 3.55E-06
vg0906286694 sf0906285694 9 6286694 NA 4.13E-06