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 mr1390 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
vg1215977007 sf1215974303 12 15977007 2.18E-221 8.59E-88
vg1210219854 sf1210217266 12 10219854 4.61E-98 2.19E-06
vg1210127313 sf1210124724 12 10127313 1.84E-95 4.44E-08
vg1209240725 sf1209238134 12 9240725 3.36E-86 NA
vg1224007541 sf1223973994 12 24007541 1.63E-85 2.12E-06
vg0217066401 sf0217060531 2 17066401 1.79E-76 NA
vg1213439429 sf1213436767 12 13439429 6.06E-75 NA
vg1215871396 sf1215868692 12 15871396 NA 1.47E-38
vg1215969757 sf1215967053 12 15969757 NA 5.63E-19
vg1216344388 sf1216341684 12 16344388 NA 2.79E-14
vg1216151894 sf1216149190 12 16151894 NA 3.95E-13
vg1215871822 sf1215869118 12 15871822 NA 8.01E-13
vg1217327067 sf1217321022 12 17327067 NA 1.49E-12
vg1216413575 sf1216410868 12 16413575 NA 9.30E-12
vg1216346285 sf1216343581 12 16346285 NA 2.48E-10
vg1216535261 sf1216532554 12 16535261 NA 3.77E-10
vg0610620315 sf0610619316 6 10620315 NA 1.24E-09
vg1215780845 sf1215778142 12 15780845 NA 1.66E-09
vg0920348485 sf0920348004 9 20348485 NA 3.67E-09
vg1215321806 sf1215319104 12 15321806 NA 3.69E-09
vg1216176025 sf1216173321 12 16176025 NA 7.09E-09
vg1214879927 sf1214877268 12 14879927 NA 1.12E-08
vg1215221436 sf1215218733 12 15221436 NA 1.23E-08
vg1216418473 sf1216415766 12 16418473 NA 2.41E-08
vg1216168602 sf1216165898 12 16168602 NA 8.22E-08
vg1216153625 sf1216150921 12 16153625 NA 8.81E-08
vg1215909724 sf1215907020 12 15909724 NA 9.42E-08
vg1216257098 sf1216254394 12 16257098 NA 1.62E-07