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 mr1129 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
vg0216803823 sf0216797953 2 16803823 5.96E-87 1.09E-33
vg0216822884 sf0216817014 2 16822884 1.15E-86 1.60E-33
vg0720349785 sf0720348792 7 20349785 4.94E-45 NA
vg0526285253 sf0526222616 5 26285253 1.55E-42 NA
vg0317475601 sf0317474383 3 17475601 2.94E-42 NA
vg0129124737 sf0129123692 1 29124737 7.78E-42 NA
vg0812023942 sf0812022947 8 12023942 1.24E-39 6.12E-12
vg0900337327 sf0900336327 9 337327 1.23E-36 2.01E-10
vg1114473442 sf1114009759 11 14473442 1.35E-36 5.28E-08
vg0213525745 sf0213525741 2 13525745 4.35E-36 1.75E-09
vg0216646507 sf0216640637 2 16646507 3.92E-35 1.31E-08
vg0216121526 sf0216115656 2 16121526 1.30E-33 2.34E-09
vg0217211213 sf0217205343 2 17211213 NA 1.59E-17
vg0217270732 sf0217264862 2 17270732 NA 1.65E-10
vg0216627796 sf0216621926 2 16627796 NA 4.95E-09
vg1005364262 sf1005380799 10 5364262 NA 1.40E-08
vg1213797573 sf1213794911 12 13797573 NA 7.32E-08
vg0216850507 sf0216844637 2 16850507 NA 1.56E-07
vg1105770829 sf1105766581 11 5770829 NA 2.11E-07
vg1114870126 sf1114406440 11 14870126 NA 1.73E-06
vg0213396747 sf0213396743 2 13396747 NA 2.02E-06
vg0618666330 sf0618665333 6 18666330 NA 2.38E-06
vg0217812733 sf0217806864 2 17812733 NA 3.23E-06
vg0404016698 sf0404012305 4 4016698 NA 3.94E-06
vg0631235279 sf0631234281 6 31235279 NA 3.95E-06