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 mr1508 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
vg1103050384 sf1103046288 11 3050384 8.40E-10 NA
vg1206782775 sf1206781665 12 6782775 2.32E-09 NA
vg0142631065 sf0142630021 1 42631065 7.26E-09 NA
vg1126312813 sf1125841226 11 26312813 1.99E-08 NA
vg0819984482 sf0819981769 8 19984482 2.16E-08 NA
vg1204504508 sf1204503496 12 4504508 4.60E-08 4.67E-06
vg0504496687 sf0504496664 5 4496687 7.98E-08 NA
vg0434773299 sf0434588190 4 34773299 1.09E-07 1.58E-07
vg0220360235 sf0220354367 2 20360235 1.88E-07 3.31E-06
vg0307814009 sf0307812947 3 7814009 3.73E-07 4.72E-06
vg1227082521 sf1227048920 12 27082521 6.15E-06 NA