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 mr1588 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
vg0804409772 sf0804408775 8 4409772 1.82E-25 NA
vg0804524150 sf0804523153 8 4524150 4.57E-25 NA
vg0402522321 sf0402517926 4 2522321 2.75E-24 NA
vg0402546694 sf0402542297 4 2546694 2.75E-24 NA
vg0807184916 sf0807183921 8 7184916 2.83E-24 NA
vg0529367142 sf0529304497 5 29367142 3.10E-24 NA
vg0319129719 sf0319128479 3 19129719 1.16E-23 NA
vg1001438303 sf1001437280 10 1438303 1.58E-23 2.16E-09
vg1001229577 sf1001228554 10 1229577 1.48E-22 1.24E-06
vg1001229450 sf1001228427 10 1229450 NA 9.75E-11
vg1002107770 sf1002106747 10 2107770 NA 9.43E-08
vg1001428076 sf1001427053 10 1428076 NA 4.55E-07
vg1002106147 sf1002105124 10 2106147 NA 4.59E-07
vg1219130121 sf1219101557 12 19130121 NA 7.80E-07
vg1219126930 sf1219098366 12 19126930 NA 9.11E-07
vg1002292435 sf1002291412 10 2292435 NA 9.38E-07
vg1217824132 sf1217795566 12 17824132 NA 3.23E-06
vg1219437108 sf1219408578 12 19437108 NA 3.54E-06
vg1000187256 sf1000186256 10 187256 NA 3.84E-06
vg0818608910 sf0818606197 8 18608910 NA 4.63E-06
vg0501179129 sf0501179113 5 1179129 NA 8.24E-06