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 mr1018 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
vg1215967225 sf1215964521 12 15967225 2.45E-134 4.45E-44
vg0621221946 sf0621220949 6 21221946 4.62E-90 4.05E-08
vg0630850632 sf0630849634 6 30850632 7.83E-87 2.45E-08
vg1221886540 sf1221853087 12 21886540 1.25E-83 9.42E-10
vg0217061679 sf0217055809 2 17061679 1.93E-83 NA
vg1210337551 sf1210334964 12 10337551 2.51E-80 2.00E-07
vg0807147308 sf0807146313 8 7147308 3.02E-79 3.12E-08
vg1219373193 sf1219344662 12 19373193 1.81E-72 2.07E-07
vg1215871396 sf1215868692 12 15871396 NA 5.64E-26
vg1215970855 sf1215968151 12 15970855 NA 8.62E-20
vg1215916036 sf1215913332 12 15916036 NA 4.33E-16
vg1216075902 sf1216073198 12 16075902 NA 1.59E-12
vg1216346285 sf1216343581 12 16346285 NA 4.96E-12
vg1216346096 sf1216343392 12 16346096 NA 2.10E-11
vg1215871822 sf1215869118 12 15871822 NA 2.72E-11
vg1216020887 sf1216018183 12 16020887 NA 1.18E-10
vg0521485463 sf0521422904 5 21485463 NA 1.40E-10
vg0610620315 sf0610619316 6 10620315 NA 3.50E-10
vg1216345874 sf1216343170 12 16345874 NA 1.14E-09
vg1215166811 sf1215164147 12 15166811 NA 1.39E-09
vg1212938220 sf1212935559 12 12938220 NA 4.70E-09
vg0920348485 sf0920348004 9 20348485 NA 1.01E-08
vg1215251809 sf1215249107 12 15251809 NA 2.00E-08
vg0408410897 sf0408406171 4 8410897 NA 5.20E-08
vg1109319597 sf1109314174 11 9319597 NA 6.42E-08
vg1216062863 sf1216060159 12 16062863 NA 6.98E-08
vg1216151894 sf1216149190 12 16151894 NA 8.09E-08
vg1215312964 sf1215310262 12 15312964 NA 2.77E-07