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 mr1261 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
vg1215959483 sf1215956779 12 15959483 1.90E-73 2.85E-18
vg1215968216 sf1215965512 12 15968216 3.31E-72 1.35E-20
vg1018571610 sf1018500167 10 18571610 2.04E-64 6.65E-10
vg0630628286 sf0630627288 6 30628286 3.33E-64 7.37E-08
vg0630850632 sf0630849634 6 30850632 3.59E-63 5.34E-08
vg0112941979 sf0112940953 1 12941979 3.42E-62 3.91E-06
vg0129572447 sf0129571402 1 29572447 4.38E-62 NA
vg0805964617 sf0805963620 8 5964617 5.21E-62 9.35E-07
vg0621221946 sf0621220949 6 21221946 5.83E-61 4.59E-07
vg1013695657 sf1013624426 10 13695657 6.24E-58 6.48E-07
vg1215969757 sf1215967053 12 15969757 NA 1.44E-15
vg1216413575 sf1216410868 12 16413575 NA 9.98E-10
vg1215871396 sf1215868692 12 15871396 NA 3.73E-09
vg1203243070 sf1203242073 12 3243070 NA 4.33E-09
vg1004591319 sf1004607857 10 4591319 NA 8.19E-09
vg1215894346 sf1215891642 12 15894346 NA 1.21E-08
vg1215390403 sf1215387701 12 15390403 NA 2.22E-08
vg1215156893 sf1215154229 12 15156893 NA 2.90E-08
vg1116068177 sf1115603049 11 16068177 NA 3.34E-08
vg1216019534 sf1216016830 12 16019534 NA 7.00E-08
vg1216557565 sf1216554858 12 16557565 NA 1.07E-07
vg0920348485 sf0920348004 9 20348485 NA 2.20E-07
vg1215321806 sf1215319104 12 15321806 NA 2.31E-07
vg1216345935 sf1216343231 12 16345935 NA 2.32E-07
vg0819075122 sf0819072409 8 19075122 NA 3.00E-07
vg1215673648 sf1215670945 12 15673648 NA 3.16E-07
vg1215187782 sf1215185118 12 15187782 NA 3.64E-07
vg0134766241 sf0134765198 1 34766241 NA 4.91E-07
vg1215126561 sf1215123897 12 15126561 NA 5.04E-07
vg0912172576 sf0912171575 9 12172576 NA 5.15E-07
vg0133494604 sf0133493560 1 33494604 NA 7.02E-07
vg1215332210 sf1215329508 12 15332210 NA 8.48E-07