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 mr1631 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
vg0405615364 sf0405610805 4 5615364 7.24E-42 1.93E-16
vg0405589223 sf0405584664 4 5589223 2.08E-41 1.70E-16
vg0308497271 sf0308496209 3 8497271 1.79E-30 NA
vg0615292681 sf0615291682 6 15292681 6.96E-29 3.45E-06
vg0523036172 sf0522973613 5 23036172 2.52E-28 NA
vg1016851622 sf1016780394 10 16851622 2.80E-28 NA
vg0410985561 sf0410976262 4 10985561 7.44E-25 2.44E-06
vg0405710877 sf0405706316 4 5710877 NA 5.66E-10
vg0405604220 sf0405599661 4 5604220 NA 1.17E-08
vg0405209631 sf0405205072 4 5209631 NA 6.49E-07
vg1219172007 sf1219143477 12 19172007 NA 1.20E-06
vg0403648569 sf0403644173 4 3648569 NA 1.45E-06
vg0405785336 sf0405780775 4 5785336 NA 2.60E-06
vg0113630238 sf0113629212 1 13630238 NA 2.64E-06
vg1004374773 sf1004391311 10 4374773 NA 2.93E-06
vg0814544220 sf0814541506 8 14544220 NA 3.87E-06
vg0405622759 sf0405618200 4 5622759 NA 4.83E-06