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 mr1980 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
vg1013626874 sf1013555644 10 13626874 1.69E-42 1.94E-19
vg1013533412 sf1013462182 10 13533412 9.10E-40 2.60E-20
vg1013729406 sf1013658175 10 13729406 9.07E-33 3.91E-13
vg0718994620 sf0718993627 7 18994620 1.76E-22 NA
vg1016127481 sf1016056253 10 16127481 1.84E-22 NA
vg0629926258 sf0629925260 6 29926258 5.80E-22 NA
vg0314998267 sf0314996914 3 14998267 7.02E-22 NA
vg1220853596 sf1220820145 12 20853596 4.12E-20 7.74E-08
vg1122952740 sf1122486611 11 22952740 6.93E-20 2.70E-06
vg1013715217 sf1013643986 10 13715217 7.01E-20 5.78E-10
vg0203433301 sf0203433299 2 3433301 2.93E-18 4.22E-07
vg0819075122 sf0819072409 8 19075122 4.76E-18 8.72E-07
vg1013280851 sf1013209620 10 13280851 NA 1.31E-11
vg1013488546 sf1013417316 10 13488546 NA 1.09E-09
vg1013800782 sf1013729551 10 13800782 NA 1.56E-08
vg1013768895 sf1013697664 10 13768895 NA 3.79E-08
vg1013692698 sf1013621467 10 13692698 NA 2.91E-07
vg1013638393 sf1013567162 10 13638393 NA 3.61E-07
vg0105393860 sf0105392860 1 5393860 NA 1.43E-06
vg1128828572 sf1128305351 11 28828572 NA 1.57E-06
vg0206119753 sf0206119753 2 6119753 NA 2.38E-06
vg1128835404 sf1128312183 11 28835404 NA 2.41E-06
vg1013527440 sf1013456210 10 13527440 NA 2.74E-06
vg0316049074 sf0316047721 3 16049074 NA 3.40E-06
vg0607991416 sf0607990417 6 7991416 NA 3.58E-06
vg1013333671 sf1013262440 10 13333671 NA 3.69E-06
vg1221714133 sf1221680680 12 21714133 NA 3.77E-06
vg0820968946 sf0820966233 8 20968946 NA 4.87E-06
vg0605613230 sf0605612231 6 5613230 NA 7.17E-06