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 mr1019 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 1.22E-92 1.63E-28
vg1215968216 sf1215965512 12 15968216 1.35E-92 5.54E-29
vg0621221946 sf0621220949 6 21221946 5.75E-70 3.90E-07
vg0631078961 sf0631077963 6 31078961 1.80E-67 2.23E-06
vg0112941979 sf0112940953 1 12941979 2.82E-66 2.01E-06
vg0113133591 sf0113132565 1 13133591 2.78E-64 1.93E-06
vg0408349202 sf0408344476 4 8349202 1.32E-63 NA
vg0807733703 sf0807732708 8 7733703 6.97E-61 8.12E-07
vg0133489903 sf0133488859 1 33489903 5.15E-57 8.41E-06
vg1215970855 sf1215968151 12 15970855 NA 2.39E-17
vg1215871396 sf1215868692 12 15871396 NA 2.53E-16
vg1215871822 sf1215869118 12 15871822 NA 1.88E-12
vg1216075902 sf1216073198 12 16075902 NA 5.61E-12
vg1215916036 sf1215913332 12 15916036 NA 7.36E-12
vg0920348485 sf0920348004 9 20348485 NA 1.54E-09
vg1215784291 sf1215781588 12 15784291 NA 2.18E-09
vg0500829493 sf0500829475 5 829493 NA 8.22E-09
vg1216019534 sf1216016830 12 16019534 NA 1.42E-08
vg1215956379 sf1215953675 12 15956379 NA 1.44E-08
vg1215825879 sf1215823176 12 15825879 NA 1.46E-08
vg1215337843 sf1215335141 12 15337843 NA 2.79E-08
vg0805363950 sf0805362953 8 5363950 NA 4.22E-08
vg1203243070 sf1203242073 12 3243070 NA 1.41E-07
vg1215161569 sf1215158905 12 15161569 NA 2.05E-07
vg0330806269 sf0330799156 3 30806269 NA 2.40E-07
vg0325046243 sf0325044323 3 25046243 NA 4.46E-07
vg1215795914 sf1215793211 12 15795914 NA 5.88E-07
vg1216127501 sf1216124797 12 16127501 NA 6.18E-07
vg1215770747 sf1215768044 12 15770747 NA 6.63E-07
vg0916572610 sf0916571609 9 16572610 NA 7.01E-07
vg1215091766 sf1215089107 12 15091766 NA 8.39E-07
vg1214381489 sf1214378830 12 14381489 NA 9.33E-07
vg1215414598 sf1215411896 12 15414598 NA 9.54E-07
vg0313544485 sf0313543203 3 13544485 NA 1.04E-06
vg0711199612 sf0711198618 7 11199612 NA 2.70E-06