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 mr1158 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
vg0404353315 sf0404348919 4 4353315 7.69E-12 NA
vg0405777618 sf0405773057 4 5777618 1.68E-11 NA
vg0700103970 sf0700102970 7 103970 2.58E-11 NA
vg0234625030 sf0234619161 2 34625030 3.87E-11 NA
vg0104860223 sf0104859223 1 4860223 1.33E-10 NA
vg1000080974 sf1000079974 10 80974 5.41E-10 6.54E-07
vg0700071969 sf0700070969 7 71969 1.10E-09 1.16E-07
vg0421038480 sf0420866534 4 21038480 2.96E-07 1.00E-06
vg1000290377 sf1000289377 10 290377 4.26E-07 3.52E-06
vg0610412797 sf0610411798 6 10412797 4.52E-07 4.71E-06
vg1000058548 sf1000057548 10 58548 8.50E-07 1.83E-06
vg1114617929 sf1114154247 11 14617929 2.97E-06 4.64E-06
vg1213556772 sf1213554110 12 13556772 6.64E-06 NA
vg1000868695 sf1000867671 10 868695 7.53E-06 2.63E-06
vg1105927934 sf1105923686 11 5927934 NA 1.75E-06