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 mr1471 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
vg0407541897 sf0407537167 4 7541897 2.08E-13 NA
vg0335630368 sf0335623237 3 35630368 2.15E-13 5.59E-06
vg0323240599 sf0323239087 3 23240599 3.26E-13 7.65E-07
vg0323186777 sf0323185265 3 23186777 3.27E-13 6.12E-07
vg0800007834 sf0800006834 8 7834 3.91E-13 2.89E-06
vg0209189237 sf0209189235 2 9189237 5.57E-13 NA
vg0233733433 sf0233727564 2 33733433 7.94E-13 4.03E-06
vg0101291884 sf0101290884 1 1291884 2.71E-12 1.43E-06
vg0800132787 sf0800131787 8 132787 2.94E-12 NA
vg0421025376 sf0420853429 4 21025376 NA 1.11E-07
vg0908755951 sf0908754950 9 8755951 NA 6.24E-07
vg0304531065 sf0304530067 3 4531065 NA 1.12E-06
vg1004450805 sf1004467343 10 4450805 NA 2.10E-06
vg0801252977 sf0801251979 8 1252977 NA 2.77E-06
vg1126800419 sf1126328806 11 26800419 NA 2.84E-06
vg1114456299 sf1113992616 11 14456299 NA 3.04E-06
vg0413260405 sf0413251115 4 13260405 NA 4.43E-06
vg0420830218 sf0420658261 4 20830218 NA 5.76E-06