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 mr1489 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 1.54E-177 1.23E-60
vg1215977133 sf1215974429 12 15977133 3.27E-155 1.57E-47
vg0621221946 sf0621220949 6 21221946 5.09E-90 8.24E-07
vg1211802220 sf1211799556 12 11802220 5.83E-89 1.26E-06
vg1018567403 sf1018495960 10 18567403 1.61E-85 6.25E-06
vg0113354243 sf0113353217 1 13354243 7.28E-85 4.10E-06
vg1018571610 sf1018500167 10 18571610 1.98E-84 3.61E-08
vg1215871396 sf1215868692 12 15871396 NA 7.85E-30
vg1215969757 sf1215967053 12 15969757 NA 2.34E-21
vg1215894346 sf1215891642 12 15894346 NA 2.98E-15
vg0610620315 sf0610619316 6 10620315 NA 1.15E-12
vg1216344665 sf1216341961 12 16344665 NA 5.47E-11
vg1216151755 sf1216149051 12 16151755 NA 8.55E-11
vg1216281909 sf1216279205 12 16281909 NA 1.12E-10
vg1215886454 sf1215883750 12 15886454 NA 1.68E-10
vg1215763538 sf1215760835 12 15763538 NA 2.21E-10
vg1216411230 sf1216408523 12 16411230 NA 2.38E-10
vg1216023976 sf1216021272 12 16023976 NA 2.42E-10
vg1216486981 sf1216484274 12 16486981 NA 2.79E-10
vg1215321806 sf1215319104 12 15321806 NA 4.50E-10
vg1216346285 sf1216343581 12 16346285 NA 1.83E-09
vg1214514841 sf1214512182 12 14514841 NA 2.17E-09
vg1215434951 sf1215432249 12 15434951 NA 2.40E-09
vg1202865605 sf1202864607 12 2865605 NA 2.77E-09
vg0408410720 sf0408405994 4 8410720 NA 8.96E-09
vg1116068177 sf1115603049 11 16068177 NA 9.21E-09
vg0702437436 sf0702436437 7 2437436 NA 1.07E-08
vg1215271479 sf1215268777 12 15271479 NA 1.51E-08
vg0123660341 sf0123659297 1 23660341 NA 1.72E-08
vg0916677066 sf0916676065 9 16677066 NA 3.63E-07