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 mr1352 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
vg0137639112 sf0137638069 1 37639112 1.05E-30 NA
vg0128560758 sf0128559713 1 28560758 5.70E-30 NA
vg0306758158 sf0306757158 3 6758158 2.66E-29 NA
vg0133415513 sf0133414469 1 33415513 4.76E-28 NA
vg0123705252 sf0123704208 1 23705252 5.20E-28 NA
vg0819378109 sf0819375396 8 19378109 2.58E-25 4.63E-06
vg0819304010 sf0819301297 8 19304010 1.02E-17 2.16E-06
vg0630306971 sf0630305973 6 30306971 6.06E-17 1.54E-06
vg0904007458 sf0904006458 9 4007458 NA 2.84E-06
vg0210641169 sf0210641167 2 10641169 NA 3.15E-06
vg0221240541 sf0221234673 2 21240541 NA 4.35E-06
vg1214600105 sf1214597445 12 14600105 NA 7.81E-06