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 mr1471 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
vg0805408311 sf0805407314 8 5408311 1.79E-14 NA
vg0434360385 sf0434175279 4 34360385 3.76E-14 NA
vg0422013922 sf0421841973 4 22013922 5.69E-14 NA
vg0801796060 sf0801795063 8 1796060 6.85E-14 NA
vg0724465961 sf0724464967 7 24465961 2.82E-13 NA
vg1118128662 sf1117662520 11 18128662 8.99E-12 3.42E-06
vg0421025376 sf0420853429 4 21025376 3.22E-11 4.90E-06
vg0207726478 sf0207726477 2 7726478 3.75E-11 2.88E-06
vg0920196604 sf0920196123 9 20196604 1.32E-10 5.92E-08
vg0706854122 sf0706853127 7 6854122 1.90E-09 3.15E-06
vg0123838334 sf0123837290 1 23838334 1.93E-08 5.69E-06
vg1115052952 sf1114589266 11 15052952 NA 8.32E-07
vg1117950562 sf1117484420 11 17950562 NA 1.29E-06
vg0114152314 sf0114151288 1 14152314 NA 5.54E-06
vg0900274113 sf0900273113 9 274113 NA 5.57E-06