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 mr1024 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
vg1010358910 sf1010287731 10 10358910 5.58E-09 5.58E-09
vg0611534900 sf0611533901 6 11534900 8.74E-09 8.74E-09
vg0200274146 sf0200274146 2 274146 9.01E-09 9.01E-09
vg1206313417 sf1206312307 12 6313417 1.60E-08 1.60E-08
vg0328044755 sf0328037809 3 28044755 1.33E-07 1.33E-07
vg0335027666 sf0335020536 3 35027666 1.59E-07 1.59E-07
vg1105855740 sf1105851492 11 5855740 8.22E-07 8.22E-07
vg0517199333 sf0517138974 5 17199333 1.23E-06 1.23E-06
vg1006079887 sf1006096424 10 6079887 2.39E-06 2.39E-06
vg0819456177 sf0819453464 8 19456177 2.62E-06 2.62E-06
vg1227357675 sf1227324075 12 27357675 2.62E-06 2.62E-06
vg1206949752 sf1206948642 12 6949752 2.65E-06 2.65E-06
vg0122995888 sf0122994844 1 22995888 2.97E-06 2.97E-06
vg1013034102 sf1012962917 10 13034102 3.06E-06 3.06E-06
vg1002853783 sf1002852760 10 2853783 3.78E-06 3.78E-06
vg0121172559 sf0121171514 1 21172559 3.84E-06 3.84E-06
vg1004346276 sf1004362814 10 4346276 3.89E-06 3.89E-06
vg0304394213 sf0304393215 3 4394213 4.37E-06 4.37E-06
vg1124826323 sf1124360163 11 24826323 4.55E-06 4.55E-06