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 mr1613 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
vg0222731119 sf0222725250 2 22731119 1.54E-16 1.31E-08
vg0222744532 sf0222738663 2 22744532 2.81E-16 1.78E-09
vg0406995300 sf0406990571 4 6995300 7.49E-11 1.30E-06
vg0406592386 sf0406587830 4 6592386 1.31E-10 4.16E-08
vg0224620629 sf0224614760 2 24620629 2.28E-10 NA
vg0223166690 sf0223160821 2 23166690 1.48E-09 2.41E-06
vg0122328226 sf0122327181 1 22328226 1.53E-09 NA
vg0406944785 sf0406940053 4 6944785 1.91E-08 4.97E-07
vg0112183141 sf0112182115 1 12183141 2.93E-08 2.88E-06
vg0406944478 sf0406939746 4 6944478 4.20E-08 3.82E-06
vg1216192863 sf1216190159 12 16192863 1.61E-07 2.02E-06
vg0811355397 sf0811354402 8 11355397 5.28E-07 4.31E-06
vg0513661910 sf0513604456 5 13661910 1.60E-06 NA
vg0618372053 sf0618371056 6 18372053 1.84E-06 NA
vg0921620411 sf0921619930 9 21620411 9.99E-06 NA
vg0407665649 sf0407660916 4 7665649 NA 3.94E-07
vg0119825736 sf0119824691 1 19825736 NA 4.95E-06