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 mr1132 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 2.84E-242 1.17E-87
vg1210219854 sf1210217266 12 10219854 7.13E-110 6.81E-06
vg1224007541 sf1223973994 12 24007541 8.22E-101 3.17E-07
vg0217092666 sf0217086796 2 17092666 1.83E-94 NA
vg0621221946 sf0621220949 6 21221946 9.46E-92 2.99E-06
vg1018571610 sf1018500167 10 18571610 1.08E-87 2.61E-10
vg1215871396 sf1215868692 12 15871396 NA 6.16E-42
vg1215969757 sf1215967053 12 15969757 NA 6.58E-29
vg1216151894 sf1216149190 12 16151894 NA 4.71E-19
vg0920348485 sf0920348004 9 20348485 NA 8.92E-14
vg1215871822 sf1215869118 12 15871822 NA 1.90E-13
vg1215962650 sf1215959946 12 15962650 NA 3.73E-13
vg1215321806 sf1215319104 12 15321806 NA 6.70E-13
vg1216153625 sf1216150921 12 16153625 NA 3.89E-12
vg1217330392 sf1217324347 12 17330392 NA 9.94E-12
vg1216165057 sf1216162353 12 16165057 NA 1.23E-11
vg1215780845 sf1215778142 12 15780845 NA 3.93E-11
vg1216535261 sf1216532554 12 16535261 NA 7.93E-11
vg1215113708 sf1215111043 12 15113708 NA 1.06E-10
vg1215763538 sf1215760835 12 15763538 NA 1.24E-10
vg1216413575 sf1216410868 12 16413575 NA 1.74E-10
vg1117717695 sf1117251551 11 17717695 NA 1.88E-10
vg0610620315 sf0610619316 6 10620315 NA 1.89E-10
vg1216346285 sf1216343581 12 16346285 NA 2.95E-10
vg1215337843 sf1215335141 12 15337843 NA 3.26E-10
vg1217302353 sf1217296308 12 17302353 NA 3.59E-10