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 mr1109 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
vg0216834788 sf0216828918 2 16834788 4.23E-94 1.72E-35
vg0217033543 sf0217027673 2 17033543 4.50E-93 1.52E-38
vg0720349785 sf0720348792 7 20349785 4.79E-60 NA
vg0525733901 sf0525671322 5 25733901 2.31E-59 NA
vg0525745525 sf0525682946 5 25745525 1.17E-58 2.15E-06
vg0504620238 sf0504620215 5 4620238 4.68E-58 NA
vg0221147432 sf0221141564 2 21147432 2.20E-57 NA
vg0812023942 sf0812022947 8 12023942 9.89E-51 9.19E-14
vg1100978684 sf1100977685 11 978684 7.82E-50 NA
vg0900336799 sf0900335799 9 336799 9.25E-48 2.62E-11
vg0523455096 sf0523392517 5 23455096 9.62E-48 NA
vg0435279519 sf0435094400 4 35279519 5.28E-47 NA
vg0217193771 sf0217187901 2 17193771 NA 3.24E-23
vg0212179963 sf0212179959 2 12179963 NA 2.61E-12
vg0216756056 sf0216750186 2 16756056 NA 4.90E-12
vg1005364262 sf1005380799 10 5364262 NA 6.29E-10
vg0217612660 sf0217606790 2 17612660 NA 1.23E-09
vg1114473442 sf1114009759 11 14473442 NA 1.76E-09
vg1112889066 sf1112425387 11 12889066 NA 1.69E-08
vg0217270732 sf0217264862 2 17270732 NA 2.35E-07
vg0908235569 sf0908234569 9 8235569 NA 3.40E-07
vg0218082294 sf0218076425 2 18082294 NA 3.72E-07
vg1208608708 sf1208606115 12 8608708 NA 7.54E-07
vg0216633239 sf0216627369 2 16633239 NA 1.23E-06
vg1105770829 sf1105766581 11 5770829 NA 1.44E-06
vg1207456492 sf1207453898 12 7456492 NA 1.52E-06
vg1010274005 sf1010202826 10 10274005 NA 1.87E-06
vg0618361629 sf0618360632 6 18361629 NA 1.89E-06
vg0216487628 sf0216481758 2 16487628 NA 2.26E-06