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 mr1446 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
vg1012428033 sf1012356848 10 12428033 9.95E-10 1.23E-07
vg1012244370 sf1012173185 10 12244370 1.42E-09 1.55E-07
vg0820147127 sf0820144414 8 20147127 3.85E-09 4.45E-08
vg1218169210 sf1218140646 12 18169210 7.94E-09 1.08E-06
vg0224478551 sf0224472682 2 24478551 1.05E-08 1.11E-07
vg0820694826 sf0820692113 8 20694826 3.80E-08 1.61E-07
vg0820747994 sf0820745281 8 20747994 8.84E-08 5.30E-07
vg0901940944 sf0901939944 9 1940944 9.66E-08 4.08E-06
vg0434330680 sf0434145574 4 34330680 1.32E-07 4.36E-07
vg1219111880 sf1219083316 12 19111880 1.99E-06 NA
vg0212825334 sf0212825330 2 12825334 2.37E-06 3.05E-06
vg0608694617 sf0608693618 6 8694617 2.73E-06 NA