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 mr1224 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
vg0719140447 sf0719139454 7 19140447 5.92E-61 2.38E-22
vg0719088274 sf0719087281 7 19088274 1.47E-54 2.41E-23
vg0719199004 sf0719198011 7 19199004 1.54E-53 3.82E-24
vg0709131140 sf0709130146 7 9131140 8.77E-43 9.53E-06
vg1201968520 sf1201967518 12 1968520 2.84E-42 NA
vg0504424645 sf0504424622 5 4424645 2.88E-42 NA
vg0918694680 sf0918693679 9 18694680 7.14E-42 NA
vg0819536015 sf0819533302 8 19536015 1.12E-38 3.67E-06
vg0819529346 sf0819526633 8 19529346 8.24E-38 NA
vg0305031973 sf0305030975 3 5031973 9.77E-38 9.24E-07
vg0719055344 sf0719054351 7 19055344 NA 2.88E-16
vg0719091461 sf0719090468 7 19091461 NA 3.76E-12
vg0222815364 sf0222809495 2 22815364 NA 7.17E-10
vg0222755345 sf0222749476 2 22755345 NA 3.23E-09
vg0718955684 sf0718954691 7 18955684 NA 4.08E-09
vg0719087589 sf0719086596 7 19087589 NA 3.51E-07
vg0230189175 sf0230183306 2 30189175 NA 6.87E-07
vg0916568531 sf0916567530 9 16568531 NA 7.45E-07
vg0719618102 sf0719617109 7 19618102 NA 7.85E-07
vg0722032999 sf0722032006 7 22032999 NA 9.27E-07
vg0724694719 sf0724693725 7 24694719 NA 1.90E-06
vg0408189411 sf0408184685 4 8189411 NA 3.45E-06