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 mr1238 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
vg1125118463 sf1124652303 11 25118463 8.01E-30 4.75E-31
vg1124875808 sf1124409648 11 24875808 9.69E-11 5.25E-11
vg1124970141 sf1124503981 11 24970141 5.01E-09 3.67E-08
vg1124223852 sf1123757722 11 24223852 3.74E-08 NA
vg0814644208 sf0814641494 8 14644208 5.13E-08 4.86E-07
vg1124991220 sf1124525060 11 24991220 5.84E-08 1.19E-11
vg0224273930 sf0224268061 2 24273930 1.16E-07 5.52E-08
vg1124931687 sf1124465527 11 24931687 2.56E-07 1.05E-07
vg1124890479 sf1124424319 11 24890479 4.02E-07 9.18E-07
vg1128817881 sf1128294660 11 28817881 5.38E-07 1.45E-06
vg1125545020 sf1125078859 11 25545020 3.49E-06 1.96E-07
vg1124948132 sf1124481972 11 24948132 NA 7.18E-07
vg1123329733 sf1122863603 11 23329733 NA 3.09E-06
vg0208287795 sf0208287794 2 8287795 NA 4.58E-06