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 mr1504 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
vg0137943961 sf0137942918 1 37943961 3.39E-118 2.12E-19
vg0138205093 sf0138204050 1 38205093 4.00E-117 1.17E-19
vg0137930104 sf0137929061 1 37930104 3.47E-116 1.19E-19
vg1119447059 sf1118980747 11 19447059 2.05E-93 NA
vg0820986552 sf0820983839 8 20986552 8.61E-90 2.73E-06
vg0327028819 sf0327021872 3 27028819 1.82E-89 NA
vg0107601240 sf0107600240 1 7601240 5.39E-89 NA
vg0821068114 sf0821065401 8 21068114 NA 2.01E-07
vg0812088790 sf0812087795 8 12088790 NA 4.23E-07
vg0305015386 sf0305014388 3 5015386 NA 6.15E-07
vg1119957243 sf1119491166 11 19957243 NA 8.02E-07
vg0141183119 sf0141182076 1 41183119 NA 1.01E-06
vg0101253853 sf0101252853 1 1253853 NA 1.37E-06
vg0821069859 sf0821067146 8 21069859 NA 1.55E-06
vg0135024184 sf0135023141 1 35024184 NA 1.83E-06
vg0141203398 sf0141202355 1 41203398 NA 2.05E-06
vg1126773646 sf1126302033 11 26773646 NA 3.86E-06
vg1116495084 sf1116029961 11 16495084 NA 3.90E-06
vg0335362475 sf0335355344 3 35362475 NA 4.55E-06
vg0101270981 sf0101269981 1 1270981 NA 6.80E-06