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 mr1248 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
vg0216657284 sf0216651414 2 16657284 5.56E-29 2.67E-11
vg0216800422 sf0216794552 2 16800422 1.57E-21 2.52E-11
vg0216673252 sf0216667382 2 16673252 9.26E-21 7.16E-09
vg0216673654 sf0216667784 2 16673654 1.77E-20 1.02E-09
vg0216773519 sf0216767649 2 16773519 1.55E-16 7.36E-09
vg0402172536 sf0402168131 4 2172536 4.78E-16 NA
vg0409778619 sf0409769317 4 9778619 1.71E-15 NA
vg1210231211 sf1210228623 12 10231211 3.24E-15 NA
vg0127216141 sf0127215097 1 27216141 1.67E-13 8.96E-07
vg0335925270 sf0335918139 3 35925270 1.79E-12 5.04E-09
vg0334445299 sf0334438169 3 34445299 NA 1.99E-12
vg0142100802 sf0142099759 1 42100802 NA 1.67E-09
vg0142085967 sf0142084924 1 42085967 NA 5.66E-09
vg0520397455 sf0520334927 5 20397455 NA 1.46E-08
vg0309123433 sf0309122369 3 9123433 NA 1.78E-08
vg1106502273 sf1106498025 11 6502273 NA 5.95E-08
vg0822296656 sf0822293943 8 22296656 NA 9.03E-08
vg0131980932 sf0131979888 1 31980932 NA 1.09E-07
vg1118715674 sf1118249482 11 18715674 NA 1.35E-07
vg0334779506 sf0334772376 3 34779506 NA 1.67E-07
vg0317967365 sf0317966147 3 17967365 NA 2.11E-07
vg0318065659 sf0318064441 3 18065659 NA 2.31E-07
vg0127596872 sf0127595828 1 27596872 NA 3.42E-07
vg0803611718 sf0803610721 8 3611718 NA 3.70E-07
vg0622468172 sf0622467175 6 22468172 NA 4.19E-07
vg0521478311 sf0521415752 5 21478311 NA 4.46E-07
vg0216789715 sf0216783845 2 16789715 NA 4.49E-07
vg0322619797 sf0322618286 3 22619797 NA 5.43E-07
vg0719509692 sf0719508699 7 19509692 NA 6.65E-07
vg0822285596 sf0822282883 8 22285596 NA 1.65E-06