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 mr1912 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
vg1105921472 sf1105917224 11 5921472 1.73E-10 7.80E-06
vg0413440235 sf0413430949 4 13440235 9.20E-10 8.34E-08
vg1222306332 sf1222272879 12 22306332 4.30E-09 9.87E-07
vg0142831977 sf0142830933 1 42831977 6.06E-09 1.57E-06
vg0131497144 sf0131496100 1 31497144 8.08E-09 NA
vg0319980220 sf0319978731 3 19980220 1.16E-07 9.33E-07
vg0117732560 sf0117731514 1 17732560 2.17E-07 4.71E-06
vg1110170506 sf1110165083 11 10170506 3.00E-07 3.18E-06
vg0616628658 sf0616627660 6 16628658 4.20E-07 1.62E-06
vg1207363214 sf1207360621 12 7363214 8.38E-07 2.94E-07
vg1221803986 sf1221770533 12 21803986 1.85E-06 NA
vg0520358656 sf0520296129 5 20358656 3.80E-06 2.69E-06
vg0114524304 sf0114523278 1 14524304 4.68E-06 NA
vg0912300788 sf0912299787 9 12300788 NA 1.73E-06
vg1205512069 sf1205511055 12 5512069 NA 4.00E-06