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 mr1561 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
vg0123467869 sf0123466825 1 23467869 2.09E-16 1.26E-06
vg0307490311 sf0307489249 3 7490311 1.64E-13 NA
vg1125786368 sf1125320289 11 25786368 1.93E-13 1.64E-07
vg1126542743 sf1126071158 11 26542743 2.71E-13 1.35E-09
vg0619445566 sf0619444569 6 19445566 2.90E-13 NA
vg0122431110 sf0122430065 1 22431110 5.17E-12 1.34E-06
vg0122433295 sf0122432250 1 22433295 1.11E-11 9.89E-07
vg1126496401 sf1126024815 11 26496401 1.32E-11 1.05E-09
vg0137928874 sf0137927831 1 37928874 3.72E-08 2.27E-06
vg0123676188 sf0123675144 1 23676188 2.11E-07 2.42E-06
vg0516005213 sf0515947721 5 16005213 3.36E-07 NA
vg1126571224 sf1126099639 11 26571224 6.99E-06 3.95E-06
vg1104329073 sf1104324975 11 4329073 7.74E-06 NA
vg0709163089 sf0709162095 7 9163089 9.07E-06 NA
vg1101201264 sf1101200265 11 1201264 NA 4.88E-07
vg0233057746 sf0233051877 2 33057746 NA 5.86E-07
vg1203635072 sf1203634071 12 3635072 NA 7.91E-06