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 mr1929 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
vg0913668910 sf0913667909 9 13668910 1.20E-10 6.15E-07
vg0139446264 sf0139445221 1 39446264 5.73E-10 1.20E-07
vg0139486814 sf0139485771 1 39486814 1.08E-09 1.53E-06
vg1118023819 sf1117557677 11 18023819 3.46E-09 NA
vg0809442889 sf0809441893 8 9442889 4.09E-09 7.30E-08
vg0138706549 sf0138705506 1 38706549 5.40E-09 9.56E-06
vg0224292652 sf0224286783 2 24292652 6.64E-09 4.40E-07
vg0301900951 sf0301899947 3 1900951 9.91E-09 7.01E-07
vg1202732210 sf1202731212 12 2732210 4.20E-08 4.64E-07
vg0727789129 sf0727788136 7 27789129 5.72E-08 8.66E-07
vg0303150829 sf0303149825 3 3150829 7.89E-08 6.20E-07
vg0307000522 sf0306999520 3 7000522 1.02E-07 1.60E-06
vg0418098488 sf0417926529 4 18098488 1.22E-07 3.52E-06
vg0624407686 sf0624406689 6 24407686 1.77E-07 4.21E-06
vg1215889308 sf1215886604 12 15889308 1.83E-07 6.44E-07
vg1212024060 sf1212021395 12 12024060 7.39E-07 3.34E-06
vg0139831768 sf0139830725 1 39831768 1.92E-06 1.44E-06
vg1013089767 sf1013018582 10 13089767 9.30E-06 NA
vg0804941325 sf0804940328 8 4941325 NA 3.34E-07
vg0211265995 sf0211265992 2 11265995 NA 3.22E-06