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 mr1937 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
vg1125885060 sf1125418979 11 25885060 3.00E-10 6.06E-06
vg0700013410 sf0700012410 7 13410 4.56E-10 NA
vg1125885112 sf1125419031 11 25885112 8.72E-10 1.12E-06
vg1117178010 sf1116711862 11 17178010 1.00E-08 NA
vg1219377796 sf1219349266 12 19377796 1.24E-08 NA
vg0113820276 sf0113819250 1 13820276 1.73E-08 NA
vg0826837403 sf0826834689 8 26837403 2.56E-08 NA
vg0919818936 sf0919818455 9 19818936 1.74E-07 NA
vg0122917286 sf0122916242 1 22917286 8.20E-06 NA
vg1218168027 sf1218139463 12 18168027 NA 2.74E-06
vg0905711051 sf0905710051 9 5711051 NA 2.78E-06
vg0103495750 sf0103494750 1 3495750 NA 2.91E-06
vg0329519334 sf0329512374 3 29519334 NA 4.34E-06