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 mr1739 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
vg0802210939 sf0802209942 8 2210939 7.83E-68 8.31E-43
vg0802211662 sf0802210665 8 2211662 3.26E-31 1.49E-33
vg0802197946 sf0802196949 8 2197946 1.48E-29 1.48E-37
vg0801799521 sf0801798524 8 1799521 9.80E-24 5.19E-12
vg0801983616 sf0801982619 8 1983616 3.14E-19 3.98E-09
vg0920611687 sf0920611206 9 20611687 8.84E-19 NA
vg0801970990 sf0801969993 8 1970990 1.02E-18 1.51E-09
vg0802112147 sf0802111150 8 2112147 2.58E-17 1.51E-09
vg1113572172 sf1113108494 11 13572172 1.20E-14 1.88E-06
vg0802410918 sf0802409921 8 2410918 9.77E-10 1.29E-06
vg0801846003 sf0801845006 8 1846003 6.52E-09 8.66E-10
vg0802411059 sf0802410062 8 2411059 1.06E-08 3.36E-07
vg0113847918 sf0113846892 1 13847918 2.18E-07 1.68E-06
vg1216034113 sf1216031409 12 16034113 3.00E-07 1.93E-07
vg0304625462 sf0304624464 3 4625462 5.04E-07 1.82E-06
vg0304640187 sf0304639189 3 4640187 NA 3.81E-07
vg0610648065 sf0610647066 6 10648065 NA 7.31E-07
vg0403881198 sf0403876802 4 3881198 NA 4.70E-06