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 mr1023 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
vg1215869969 sf1215867265 12 15869969 1.68E-181 3.55E-52
vg1215977182 sf1215974478 12 15977182 7.83E-159 6.70E-47
vg1210581248 sf1210578661 12 10581248 1.89E-89 NA
vg1224007541 sf1223973994 12 24007541 8.65E-81 NA
vg1018567403 sf1018495960 10 18567403 1.65E-79 NA
vg0217092666 sf0217086796 2 17092666 1.66E-78 NA
vg1214293828 sf1214291168 12 14293828 1.18E-77 8.79E-12
vg1215871396 sf1215868692 12 15871396 NA 9.68E-29
vg1215969757 sf1215967053 12 15969757 NA 6.98E-16
vg1215893630 sf1215890926 12 15893630 NA 2.62E-15
vg0610620315 sf0610619316 6 10620315 NA 3.86E-11
vg1214399949 sf1214397290 12 14399949 NA 4.96E-11
vg1216082180 sf1216079476 12 16082180 NA 1.30E-10
vg1216153625 sf1216150921 12 16153625 NA 1.32E-10
vg1215321806 sf1215319104 12 15321806 NA 2.54E-10
vg1216512330 sf1216509623 12 16512330 NA 1.51E-09
vg1216165057 sf1216162353 12 16165057 NA 3.39E-09
vg1215886454 sf1215883750 12 15886454 NA 3.65E-09
vg1216413575 sf1216410868 12 16413575 NA 9.55E-09
vg1215673648 sf1215670945 12 15673648 NA 1.02E-08
vg1216344388 sf1216341684 12 16344388 NA 1.11E-08
vg1215976560 sf1215973856 12 15976560 NA 1.89E-08
vg1215271479 sf1215268777 12 15271479 NA 2.36E-08
vg1216037905 sf1216035201 12 16037905 NA 2.81E-08
vg1123486862 sf1123020732 11 23486862 NA 3.65E-08
vg1216411230 sf1216408523 12 16411230 NA 4.53E-08
vg1216059532 sf1216056828 12 16059532 NA 7.16E-08
vg1215126561 sf1215123897 12 15126561 NA 1.74E-07
vg1214417086 sf1214414427 12 14417086 NA 1.86E-07