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 mr1770 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
vg0115989167 sf0115988141 1 15989167 1.25E-17 6.22E-08
vg0910197736 sf0910196735 9 10197736 3.73E-16 NA
vg0132526029 sf0132524985 1 32526029 6.34E-16 2.34E-06
vg0501151102 sf0501151086 5 1151102 8.89E-16 NA
vg0419847240 sf0419675276 4 19847240 1.47E-15 NA
vg0132625732 sf0132624688 1 32625732 3.96E-15 7.34E-07
vg0608088741 sf0608087742 6 8088741 6.76E-14 4.96E-06
vg0224690328 sf0224684459 2 24690328 8.26E-13 4.18E-06
vg0220225964 sf0220220096 2 20225964 NA 3.13E-07
vg0800076023 sf0800075023 8 76023 NA 4.65E-06
vg0134937509 sf0134936466 1 34937509 NA 5.44E-06
vg0220811012 sf0220805144 2 20811012 NA 8.06E-06