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 mr1925 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
vg0106730666 sf0106729666 1 6730666 1.62E-33 5.09E-26
vg0106684586 sf0106683586 1 6684586 6.71E-19 3.54E-12
vg0106683798 sf0106682798 1 6683798 1.39E-17 3.24E-12
vg0105519810 sf0105518810 1 5519810 1.79E-15 2.80E-06
vg0105607941 sf0105606941 1 5607941 1.31E-14 1.23E-08
vg0107100004 sf0107099004 1 7100004 9.36E-14 6.45E-07
vg0130455488 sf0130454444 1 30455488 5.57E-13 NA
vg0105394768 sf0105393768 1 5394768 1.47E-10 2.96E-06
vg0106703618 sf0106702618 1 6703618 2.08E-10 7.86E-09
vg0316912605 sf0316911479 3 16912605 1.00E-07 NA
vg0714102855 sf0714101862 7 14102855 1.41E-07 NA
vg1125085953 sf1124619793 11 25085953 2.32E-07 1.71E-08
vg1124963993 sf1124497833 11 24963993 5.64E-07 1.83E-06
vg0105632780 sf0105631780 1 5632780 6.68E-07 1.90E-08
vg0106651186 sf0106650186 1 6651186 6.69E-07 5.77E-09
vg0110290364 sf0110289340 1 10290364 1.21E-06 5.65E-09
vg1222361978 sf1222328417 12 22361978 1.48E-06 NA
vg0106923867 sf0106922867 1 6923867 NA 9.19E-10
vg1000642191 sf1000641167 10 642191 NA 7.06E-08
vg0310142739 sf0310141675 3 10142739 NA 8.82E-08
vg0310499546 sf0310498462 3 10499546 NA 2.43E-07
vg1125118463 sf1124652303 11 25118463 NA 2.59E-07
vg1125468295 sf1125002134 11 25468295 NA 4.04E-07
vg0618478943 sf0618477946 6 18478943 NA 1.27E-06
vg0106048931 sf0106047931 1 6048931 NA 1.62E-06
vg0124514339 sf0124513295 1 24514339 NA 2.38E-06
vg1125113390 sf1124647230 11 25113390 NA 2.90E-06
vg0827118358 sf0827115644 8 27118358 NA 4.08E-06
vg0208829098 sf0208829096 2 8829098 NA 4.27E-06
vg0702607802 sf0702606803 7 2607802 NA 9.43E-06