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 mr1186 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
vg0726949917 sf0726948923 7 26949917 6.85E-09 NA
vg1126312813 sf1125841226 11 26312813 1.35E-08 NA
vg0141747523 sf0141746480 1 41747523 2.19E-08 NA
vg1207704220 sf1207701624 12 7704220 2.96E-08 NA
vg0123708079 sf0123707035 1 23708079 3.52E-08 NA
vg0725489607 sf0725488613 7 25489607 7.21E-08 NA
vg0220941121 sf0220935253 2 20941121 4.30E-07 7.46E-06
vg0403204105 sf0403199708 4 3204105 6.83E-07 1.57E-07
vg0232208358 sf0232202489 2 32208358 6.96E-07 4.69E-06
vg1216110511 sf1216107807 12 16110511 NA 1.30E-06
vg0232481318 sf0232475449 2 32481318 NA 4.21E-06
vg1118128320 sf1117662178 11 18128320 NA 6.60E-06
vg0221240541 sf0221234673 2 21240541 NA 6.93E-06