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 mr1247 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 1.55E-52 3.40E-21
vg0222687716 sf0222681847 2 22687716 1.88E-49 1.74E-21
vg0526722696 sf0526660054 5 26722696 1.16E-35 3.15E-07
vg0518201525 sf0518141011 5 18201525 6.33E-32 4.54E-07
vg1110783636 sf1110778181 11 10783636 1.07E-31 6.94E-07
vg0818186893 sf0818184180 8 18186893 1.07E-31 8.91E-08
vg1110750361 sf1110744906 11 10750361 1.85E-31 9.70E-10
vg0818212763 sf0818210050 8 18212763 5.36E-31 8.50E-09
vg0500664660 sf0500664660 5 664660 2.80E-29 1.39E-09
vg0716599841 sf0716598848 7 16599841 1.59E-27 7.59E-09
vg0222741463 sf0222735594 2 22741463 1.56E-26 6.45E-10
vg0922708358 sf0922707877 9 22708358 5.20E-26 1.01E-07
vg0222732157 sf0222726288 2 22732157 7.74E-26 4.68E-10
vg1006506535 sf1006522158 10 6506535 1.26E-23 8.90E-08
vg0431376032 sf0431190928 4 31376032 NA 4.11E-10
vg1000205246 sf1000204246 10 205246 NA 1.58E-09
vg0222271516 sf0222265647 2 22271516 NA 3.50E-09
vg0222952563 sf0222946694 2 22952563 NA 4.30E-09
vg0709372324 sf0709371330 7 9372324 NA 7.95E-09
vg0224793205 sf0224787336 2 24793205 NA 9.37E-09
vg1005950387 sf1005966925 10 5950387 NA 1.26E-08
vg0922265212 sf0922264731 9 22265212 NA 2.20E-08
vg0224791280 sf0224785411 2 24791280 NA 2.81E-08
vg0822600721 sf0822598008 8 22600721 NA 8.84E-08
vg0513252496 sf0513195418 5 13252496 NA 1.15E-07
vg0222722554 sf0222716685 2 22722554 NA 1.31E-07
vg1021149005 sf1021077484 10 21149005 NA 1.38E-07
vg0207115454 sf0207115454 2 7115454 NA 1.87E-07
vg0626215297 sf0626214300 6 26215297 NA 1.96E-07
vg0818684033 sf0818681320 8 18684033 NA 2.38E-06
vg0804869267 sf0804868270 8 4869267 NA 3.42E-06
vg0323895795 sf0323893969 3 23895795 NA 9.81E-06