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 mr1438 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
vg0615097742 sf0615096743 6 15097742 1.13E-08 1.94E-08
vg0124687217 sf0124686173 1 24687217 2.97E-08 3.55E-08
vg0429686232 sf0429501100 4 29686232 3.71E-08 1.55E-07
vg1215498700 sf1215495997 12 15498700 7.20E-08 2.76E-07
vg1215675808 sf1215673105 12 15675808 9.92E-08 1.68E-06
vg0400770969 sf0400769969 4 770969 4.64E-07 1.46E-06
vg0429628150 sf0429443018 4 29628150 6.34E-07 3.01E-07
vg1215237373 sf1215234670 12 15237373 1.80E-06 1.02E-06
vg0136979159 sf0136978116 1 36979159 4.24E-06 3.90E-06
vg1218108461 sf1218079897 12 18108461 NA 2.07E-06