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 mr1206 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
vg0903223470 sf0903222470 9 3223470 8.08E-12 NA
vg0810597423 sf0810596427 8 10597423 2.15E-11 2.46E-06
vg0108724297 sf0108723297 1 8724297 1.16E-10 NA
vg1125628490 sf1125162329 11 25628490 1.28E-10 2.83E-06
vg0207267058 sf0207267058 2 7267058 1.35E-10 1.79E-06
vg1001364496 sf1001363473 10 1364496 4.15E-10 3.76E-06
vg0132892731 sf0132891687 1 32892731 2.89E-09 6.16E-07
vg1218168027 sf1218139463 12 18168027 7.60E-09 2.64E-07
vg0422542724 sf0422357611 4 22542724 6.15E-08 6.23E-07
vg0204867231 sf0204867228 2 4867231 8.05E-08 NA
vg0819199007 sf0819196294 8 19199007 1.88E-07 NA
vg1213935504 sf1213932842 12 13935504 NA 1.86E-06
vg1209487317 sf1209484726 12 9487317 NA 3.68E-06
vg1013275525 sf1013204295 10 13275525 NA 4.43E-06