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 mr1226 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 8.14E-34 4.23E-29
vg0107214556 sf0107213556 1 7214556 6.23E-14 1.19E-07
vg0107198487 sf0107197487 1 7198487 1.04E-13 1.52E-08
vg0719056561 sf0719055568 7 19056561 2.63E-13 3.93E-24
vg0408294186 sf0408289460 4 8294186 5.11E-13 4.97E-09
vg0408293770 sf0408289044 4 8293770 6.40E-13 3.78E-09
vg0417642687 sf0417470728 4 17642687 3.68E-12 3.63E-08
vg0912061274 sf0912060273 9 12061274 5.28E-12 3.23E-07
vg0907121871 sf0907120871 9 7121871 1.01E-11 1.22E-08
vg1101911438 sf1101910439 11 1911438 1.51E-11 1.78E-10
vg0700416280 sf0700415280 7 416280 3.94E-11 8.30E-09
vg1020494793 sf1020423272 10 20494793 1.84E-10 1.91E-07
vg1213429246 sf1213426584 12 13429246 2.04E-10 3.82E-07
vg0200846970 sf0200846970 2 846970 2.17E-10 1.20E-07
vg1217240367 sf1217234322 12 17240367 2.59E-10 6.51E-07
vg0422855440 sf0422670325 4 22855440 6.68E-09 6.21E-07
vg0817806141 sf0817803428 8 17806141 8.89E-08 3.62E-07
vg0430077438 sf0429892309 4 30077438 1.07E-07 NA
vg0804028565 sf0804027568 8 4028565 1.77E-07 4.10E-07
vg0124647921 sf0124646877 1 24647921 1.64E-06 5.12E-08
vg0828401472 sf0828398758 8 28401472 NA 3.42E-08
vg0435372935 sf0435187817 4 35372935 NA 1.83E-07
vg0329561125 sf0329554165 3 29561125 NA 3.72E-07
vg1217303672 sf1217297627 12 17303672 NA 5.08E-07
vg0131510210 sf0131509166 1 31510210 NA 5.84E-07