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 mr1107 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
vg0719006525 sf0719005532 7 19006525 2.58E-22 2.01E-21
vg0719079366 sf0719078373 7 19079366 8.05E-22 3.63E-21
vg0719039736 sf0719038743 7 19039736 8.40E-11 4.43E-17
vg0408294186 sf0408289460 4 8294186 2.22E-09 5.49E-08
vg0107214556 sf0107213556 1 7214556 3.85E-09 5.19E-06
vg0107198487 sf0107197487 1 7198487 3.90E-09 5.68E-07
vg1101911438 sf1101910439 11 1911438 7.54E-09 9.93E-09
vg0700416280 sf0700415280 7 416280 7.58E-09 8.36E-09
vg0118565792 sf0118564746 1 18565792 9.95E-09 9.99E-07
vg0309326904 sf0309325840 3 9326904 1.13E-08 1.75E-06
vg1217240367 sf1217234322 12 17240367 1.16E-08 2.56E-07
vg0124676757 sf0124675713 1 24676757 1.71E-08 3.64E-09
vg0907121871 sf0907120871 9 7121871 3.49E-08 4.59E-07
vg0422489098 sf0422303985 4 22489098 6.82E-08 1.34E-08
vg0113185672 sf0113184646 1 13185672 8.93E-08 5.79E-07
vg1205863442 sf1205862424 12 5863442 2.04E-07 3.96E-08
vg1103514429 sf1103510332 11 3514429 2.34E-07 1.95E-07
vg0419906492 sf0419734528 4 19906492 2.83E-07 6.39E-07
vg0625303878 sf0625302881 6 25303878 1.98E-06 1.80E-06
vg0828401472 sf0828398758 8 28401472 NA 2.34E-08
vg0809666825 sf0809665829 8 9666825 NA 1.13E-06
vg0715273808 sf0715272815 7 15273808 NA 1.77E-06