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 mr1094 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
vg0610566237 sf0610565238 6 10566237 1.07E-36 1.58E-23
vg0612017410 sf0612016411 6 12017410 2.83E-14 4.17E-06
vg0616573244 sf0616572246 6 16573244 3.35E-14 2.26E-06
vg0613288089 sf0613287090 6 13288089 5.73E-14 6.36E-07
vg0616988304 sf0616987307 6 16988304 6.19E-14 8.05E-08
vg0719206537 sf0719205544 7 19206537 1.00E-13 9.71E-06
vg0617845062 sf0617844065 6 17845062 2.26E-13 8.27E-07
vg0610469500 sf0610468501 6 10469500 2.63E-13 4.95E-06
vg0611882368 sf0611881369 6 11882368 6.65E-13 3.21E-07
vg0613160613 sf0613159614 6 13160613 9.41E-13 7.89E-07
vg0610642043 sf0610641044 6 10642043 4.76E-10 3.88E-12
vg0222727946 sf0222722077 2 22727946 1.27E-09 1.62E-11
vg0222730004 sf0222724135 2 22730004 1.63E-09 3.75E-11
vg0610287062 sf0610286063 6 10287062 2.62E-09 1.70E-09
vg0611098317 sf0611097318 6 11098317 6.24E-09 4.72E-08
vg0610462354 sf0610461355 6 10462354 7.60E-09 1.13E-07
vg0610684751 sf0610683752 6 10684751 8.15E-09 1.28E-06
vg0122730320 sf0122729276 1 22730320 6.86E-08 5.14E-07
vg0613062563 sf0613061564 6 13062563 1.98E-07 1.64E-06
vg0334809884 sf0334802754 3 34809884 3.55E-07 4.44E-06
vg0415210679 sf0415201394 4 15210679 1.26E-06 2.07E-06
vg0610752378 sf0610751379 6 10752378 NA 5.30E-08
vg0612288311 sf0612287312 6 12288311 NA 4.41E-06
vg0408367382 sf0408362656 4 8367382 NA 4.53E-06
vg0222799001 sf0222793132 2 22799001 NA 4.90E-06