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 mr1083 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 2.68E-34 4.43E-26
vg0107214556 sf0107213556 1 7214556 4.08E-16 7.22E-09
vg0700416280 sf0700415280 7 416280 8.84E-14 3.27E-10
vg0912061274 sf0912060273 9 12061274 1.61E-13 1.82E-08
vg0907121871 sf0907120871 9 7121871 4.25E-12 6.67E-08
vg0408294186 sf0408289460 4 8294186 6.08E-12 1.02E-07
vg0309326904 sf0309325840 3 9326904 1.00E-11 3.01E-07
vg0200846970 sf0200846970 2 846970 1.45E-11 4.68E-08
vg0514963706 sf0514906249 5 14963706 2.90E-11 2.98E-07
vg1101911438 sf1101910439 11 1911438 1.62E-10 7.00E-08
vg0517655898 sf0517595540 5 17655898 4.52E-10 6.75E-07
vg0113186086 sf0113185060 1 13186086 1.50E-09 4.89E-07
vg0709019375 sf0709018381 7 9019375 1.60E-09 1.61E-07
vg0705107520 sf0705106521 7 5107520 1.61E-09 3.23E-08
vg0804028565 sf0804027568 8 4028565 2.18E-09 3.13E-08
vg0124339287 sf0124338243 1 24339287 3.39E-09 4.91E-07
vg0203976342 sf0203976339 2 3976342 1.01E-08 2.40E-07
vg0816207802 sf0816205088 8 16207802 3.55E-08 7.87E-07
vg0719129893 sf0719128900 7 19129893 1.30E-06 7.00E-16
vg0719199004 sf0719198011 7 19199004 2.33E-06 2.44E-14
vg0622463338 sf0622462341 6 22463338 3.86E-06 6.56E-07
vg0828401472 sf0828398758 8 28401472 NA 3.22E-09
vg0131510210 sf0131509166 1 31510210 NA 4.78E-07
vg0435372935 sf0435187817 4 35372935 NA 6.47E-07
vg0419763927 sf0419591962 4 19763927 NA 1.08E-06