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 mr1558 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
vg1020599607 sf1020528086 10 20599607 2.89E-19 1.42E-11
vg1102677343 sf1102673247 11 2677343 1.17E-12 1.20E-07
vg1211969945 sf1211967280 12 11969945 2.66E-11 NA
vg0805283944 sf0805282947 8 5283944 3.65E-11 3.06E-06
vg1209419991 sf1209417400 12 9419991 1.59E-10 NA
vg0920272507 sf0920272026 9 20272507 1.83E-10 6.71E-07
vg1213717956 sf1213715294 12 13717956 3.46E-08 3.35E-06
vg0707065048 sf0707064053 7 7065048 6.26E-08 NA
vg0605702164 sf0605701165 6 5702164 9.13E-08 2.53E-07
vg0817465290 sf0817462576 8 17465290 4.95E-06 NA