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 mr1750 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
vg0321369281 sf0321367791 3 21369281 3.80E-184 4.11E-32
vg0317723555 sf0317722337 3 17723555 1.01E-168 1.05E-21
vg0317750910 sf0317749692 3 17750910 1.18E-167 8.34E-23
vg0330461904 sf0330454793 3 30461904 2.02E-138 NA
vg0323964385 sf0323962559 3 23964385 3.30E-138 1.97E-06
vg0327701968 sf0327695021 3 27701968 2.33E-134 3.46E-08
vg0230169248 sf0230163379 2 30169248 2.05E-122 2.74E-06
vg0324235711 sf0324233790 3 24235711 5.00E-121 7.29E-08
vg0717005975 sf0717004982 7 17005975 3.74E-114 1.39E-06
vg0917927607 sf0917926606 9 17927607 NA 7.54E-08
vg0419738339 sf0419566374 4 19738339 NA 1.06E-07
vg0220931247 sf0220925379 2 20931247 NA 4.36E-07
vg1204336548 sf1204335536 12 4336548 NA 5.56E-07
vg0523273054 sf0523210475 5 23273054 NA 1.30E-06
vg1209081295 sf1209078704 12 9081295 NA 2.12E-06
vg0501584678 sf0501584662 5 1584678 NA 2.20E-06
vg0815172680 sf0815169966 8 15172680 NA 4.76E-06
vg1101177321 sf1101176322 11 1177321 NA 4.93E-06