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 mr1120 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
vg0222679274 sf0222673405 2 22679274 1.59E-49 6.16E-19
vg0526722696 sf0526660054 5 26722696 8.81E-33 1.82E-06
vg0818212763 sf0818210050 8 18212763 1.78E-31 1.68E-08
vg1110347259 sf1110341836 11 10347259 2.61E-30 2.94E-07
vg0503510616 sf0503510593 5 3510616 5.98E-30 NA
vg1110750361 sf1110744906 11 10750361 4.68E-29 4.59E-08
vg0500664660 sf0500664660 5 664660 7.77E-29 1.45E-07
vg0624499979 sf0624498982 6 24499979 3.75E-28 4.25E-07
vg0335918912 sf0335911781 3 35918912 7.42E-26 4.09E-07
vg0907026290 sf0907025290 9 7026290 4.25E-25 2.88E-07
vg1117963441 sf1117497299 11 17963441 2.76E-23 1.42E-07
vg0431376032 sf0431190928 4 31376032 NA 1.83E-09
vg0315713125 sf0315711772 3 15713125 NA 9.97E-09
vg0222735698 sf0222729829 2 22735698 NA 2.34E-08
vg0222741463 sf0222735594 2 22741463 NA 2.81E-08
vg1005950387 sf1005966925 10 5950387 NA 3.60E-08
vg0222952563 sf0222946694 2 22952563 NA 3.94E-08
vg0709453116 sf0709452122 7 9453116 NA 4.21E-08
vg1204507349 sf1204506337 12 4507349 NA 4.74E-08
vg0224793205 sf0224787336 2 24793205 NA 5.15E-08
vg0207115454 sf0207115454 2 7115454 NA 7.27E-08
vg0709837237 sf0709836243 7 9837237 NA 8.51E-08
vg0140883886 sf0140882843 1 40883886 NA 1.12E-07
vg1000205246 sf1000204246 10 205246 NA 1.45E-07
vg0220994638 sf0220988770 2 20994638 NA 1.86E-07
vg0819594931 sf0819592218 8 19594931 NA 2.01E-07
vg0709372324 sf0709371330 7 9372324 NA 3.54E-07
vg0222271516 sf0222265647 2 22271516 NA 4.11E-07
vg1006570950 sf1006586573 10 6570950 NA 4.42E-07
vg0224246969 sf0224241100 2 24246969 NA 5.04E-07
vg0725440295 sf0725439301 7 25440295 NA 1.00E-06
vg1122032106 sf1121565977 11 22032106 NA 1.94E-06
vg0307948436 sf0307947374 3 7948436 NA 6.90E-06