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 mr1246 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
vg0719011406 sf0719010413 7 19011406 4.26E-108 6.85E-26
vg0917918788 sf0917917787 9 17918788 7.99E-89 NA
vg1201339510 sf1201338510 12 1339510 7.27E-85 NA
vg0708225849 sf0708224854 7 8225849 2.99E-84 NA
vg0305031973 sf0305030975 3 5031973 1.70E-83 1.64E-09
vg0719278912 sf0719277919 7 19278912 6.10E-82 2.23E-11
vg0917788203 sf0917787202 9 17788203 7.99E-81 8.45E-07
vg1201345845 sf1201344845 12 1345845 2.42E-80 8.27E-07
vg0719297467 sf0719296474 7 19297467 3.27E-78 1.60E-27
vg0707515285 sf0707514290 7 7515285 1.81E-77 1.38E-06
vg0719091461 sf0719090468 7 19091461 NA 1.93E-25
vg0718955684 sf0718954691 7 18955684 NA 6.10E-15
vg0719079053 sf0719078060 7 19079053 NA 1.19E-14
vg0719045166 sf0719044173 7 19045166 NA 6.91E-13
vg0719087589 sf0719086596 7 19087589 NA 4.72E-11
vg0718885795 sf0718884802 7 18885795 NA 1.57E-09
vg0719344789 sf0719343796 7 19344789 NA 2.78E-08
vg0718914481 sf0718913488 7 18914481 NA 7.03E-08
vg0719618102 sf0719617109 7 19618102 NA 1.27E-07
vg0726127290 sf0726126296 7 26127290 NA 2.54E-07
vg0718996077 sf0718995084 7 18996077 NA 6.76E-07
vg0718982411 sf0718981418 7 18982411 NA 8.93E-07
vg0722032999 sf0722032006 7 22032999 NA 1.08E-06
vg0719140779 sf0719139786 7 19140779 NA 1.19E-06
vg0719466615 sf0719465622 7 19466615 NA 1.64E-06
vg0719491368 sf0719490375 7 19491368 NA 2.00E-06
vg0714470500 sf0714469507 7 14470500 NA 3.13E-06
vg0718960800 sf0718959807 7 18960800 NA 4.29E-06