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 mr1236 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
vg0217792183 sf0217786314 2 17792183 3.16E-21 3.99E-11
vg0217015474 sf0217009604 2 17015474 1.69E-20 2.38E-13
vg1114596727 sf1114133045 11 14596727 4.96E-17 1.17E-07
vg0900337342 sf0900336342 9 337342 8.09E-16 8.95E-08
vg0216762005 sf0216756135 2 16762005 1.15E-12 3.82E-08
vg1207456492 sf1207453898 12 7456492 1.27E-12 9.34E-07
vg0610865756 sf0610864757 6 10865756 9.36E-12 3.23E-06
vg1117550939 sf1117084795 11 17550939 1.69E-10 1.50E-06
vg1005364864 sf1005381401 10 5364864 6.02E-10 2.13E-06
vg0217365823 sf0217359953 2 17365823 1.54E-09 4.10E-07
vg0106743514 sf0106742514 1 6743514 1.86E-08 3.84E-06
vg0141980941 sf0141979898 1 41980941 1.99E-07 NA
vg1118344757 sf1117878615 11 18344757 3.21E-07 NA
vg1125773021 sf1125306860 11 25773021 7.83E-07 NA
vg0710362096 sf0710361102 7 10362096 2.59E-06 3.34E-06
vg1221718597 sf1221685144 12 21718597 5.40E-06 NA
vg1210110384 sf1210107795 12 10110384 8.48E-06 NA