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 mr1354 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
vg0429941249 sf0429756116 4 29941249 2.21E-13 7.48E-06
vg0429945960 sf0429760827 4 29945960 1.47E-12 2.93E-06
vg1119157316 sf1118691004 11 19157316 3.13E-11 NA
vg0427157594 sf0426972464 4 27157594 9.25E-11 NA
vg1119158633 sf1118692321 11 19158633 2.20E-10 2.08E-06
vg0724669663 sf0724668669 7 24669663 2.34E-10 6.25E-07
vg0330838182 sf0330831069 3 30838182 3.15E-10 NA
vg0331299298 sf0331292183 3 31299298 9.11E-09 2.13E-06
vg0916209376 sf0916208375 9 16209376 1.66E-08 1.63E-07
vg0916234298 sf0916233297 9 16234298 2.24E-08 2.56E-07
vg0724674424 sf0724673430 7 24674424 2.53E-08 4.94E-06
vg0724446330 sf0724445336 7 24446330 4.99E-08 3.99E-07
vg0724425310 sf0724424316 7 24425310 7.82E-08 1.83E-07
vg0217653452 sf0217647582 2 17653452 7.58E-06 NA
vg1019751150 sf1019679650 10 19751150 NA 9.74E-07
vg1116842221 sf1116377100 11 16842221 NA 2.57E-06
vg0624726893 sf0624725896 6 24726893 NA 4.89E-06