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 mr1542 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
vg0314567323 sf0314566010 3 14567323 3.80E-134 6.94E-89
vg0314577463 sf0314576150 3 14577463 2.99E-74 1.98E-57
vg0314512032 sf0314510720 3 14512032 1.01E-22 3.05E-21
vg0314644172 sf0314642859 3 14644172 5.70E-19 2.01E-07
vg0314884097 sf0314882744 3 14884097 1.08E-18 5.21E-09
vg0314644181 sf0314642868 3 14644181 1.67E-18 5.29E-08
vg0314884035 sf0314882682 3 14884035 2.73E-17 4.22E-10
vg0314639120 sf0314637807 3 14639120 7.67E-17 5.23E-07
vg0314638773 sf0314637460 3 14638773 3.50E-16 7.87E-07
vg0314575975 sf0314574662 3 14575975 1.73E-15 4.19E-06
vg0314579234 sf0314577921 3 14579234 3.31E-13 5.31E-12
vg0315426336 sf0315424983 3 15426336 3.88E-12 9.42E-07
vg0314510532 sf0314509220 3 14510532 6.74E-11 9.41E-09
vg0316482623 sf0316481268 3 16482623 1.96E-10 1.00E-06
vg0314726805 sf0314725492 3 14726805 7.53E-09 1.00E-06
vg0519769410 sf0519706894 5 19769410 4.68E-06 NA
vg0314544054 sf0314542742 3 14544054 NA 6.24E-12
vg0314687874 sf0314686561 3 14687874 NA 2.33E-06