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 mr1660 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
vg1013737644 sf1013666413 10 13737644 2.42E-12 5.57E-06
vg0501493417 sf0501493401 5 1493417 4.82E-12 NA
vg1013736780 sf1013665549 10 13736780 5.01E-12 9.25E-06
vg0821309836 sf0821307123 8 21309836 5.82E-12 4.83E-06
vg0629489803 sf0629488805 6 29489803 7.86E-12 NA
vg0620619367 sf0620618370 6 20619367 1.06E-11 5.96E-06
vg1010595641 sf1010524462 10 10595641 1.75E-11 1.23E-06
vg1207996233 sf1207993639 12 7996233 3.23E-09 NA
vg0421981807 sf0421809858 4 21981807 6.10E-09 NA
vg0404985775 sf0404981214 4 4985775 1.73E-08 NA
vg1010567320 sf1010496141 10 10567320 NA 1.61E-06