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 mr1495 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
vg1006839627 sf1006855250 10 6839627 1.50E-38 5.75E-14
vg1007564483 sf1007580095 10 7564483 5.91E-38 2.52E-17
vg1009620429 sf1009549250 10 9620429 4.55E-28 1.40E-07
vg1009514085 sf1009442906 10 9514085 1.06E-27 4.72E-12
vg0407825796 sf0407821064 4 7825796 2.64E-26 6.74E-10
vg0407826743 sf0407822011 4 7826743 2.95E-26 3.55E-11
vg1216843191 sf1216837145 12 16843191 1.13E-25 3.78E-11
vg0407824609 sf0407819877 4 7824609 1.62E-25 5.44E-08
vg0142683989 sf0142682945 1 42683989 5.32E-24 1.17E-07
vg0403204395 sf0403199998 4 3204395 1.62E-22 5.36E-07
vg0813652248 sf0813649533 8 13652248 2.27E-21 6.30E-08
vg1204314449 sf1204313437 12 4314449 8.55E-21 2.92E-06
vg0528706863 sf0528644218 5 28706863 2.96E-20 8.41E-08
vg1002973972 sf1002972949 10 2973972 3.05E-20 5.41E-08
vg0116924780 sf0116923734 1 16924780 9.22E-20 4.03E-06
vg0716828374 sf0716827381 7 16828374 4.19E-19 7.74E-07
vg1010383201 sf1010312022 10 10383201 1.06E-18 4.08E-06
vg0222726563 sf0222720694 2 22726563 1.40E-18 9.49E-12
vg0403206982 sf0403202585 4 3206982 4.88E-18 1.89E-07
vg0620323442 sf0620322445 6 20323442 8.33E-18 1.34E-06
vg0222727819 sf0222721950 2 22727819 9.18E-18 1.93E-10
vg0710897646 sf0710896652 7 10897646 9.84E-18 8.01E-07
vg1005615999 sf1005632537 10 5615999 1.67E-11 1.98E-06
vg0222799001 sf0222793132 2 22799001 NA 1.33E-07
vg1007752734 sf1007768343 10 7752734 NA 3.44E-06