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 mr1112 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
vg0610648813 sf0610647814 6 10648813 3.18E-12 1.49E-10
vg0610752378 sf0610751379 6 10752378 7.07E-12 1.23E-10
vg0403922278 sf0403917884 4 3922278 5.51E-09 3.01E-07
vg0809578434 sf0809577438 8 9578434 8.97E-09 3.63E-08
vg1122416969 sf1121950840 11 22416969 1.13E-08 3.51E-07
vg1224247892 sf1224214345 12 24247892 1.44E-08 4.36E-06
vg0626895745 sf0626894748 6 26895745 6.92E-08 8.93E-07
vg0610460953 sf0610459954 6 10460953 2.45E-07 2.60E-06
vg1217835762 sf1217807196 12 17835762 3.31E-07 3.51E-06
vg0817249650 sf0817246936 8 17249650 4.03E-07 4.14E-06
vg0129165747 sf0129164702 1 29165747 4.09E-07 4.40E-06
vg1215153650 sf1215150986 12 15153650 1.45E-06 1.99E-06
vg1215507555 sf1215504852 12 15507555 1.65E-06 6.11E-07
vg1206162924 sf1206161815 12 6162924 2.32E-06 8.57E-07
vg0807758172 sf0807757176 8 7758172 3.64E-06 3.60E-06
vg0509045794 sf0509045722 5 9045794 7.04E-06 3.95E-06
vg1124646669 sf1124180509 11 24646669 9.44E-06 NA
vg1203702115 sf1203701114 12 3702115 NA 9.85E-07