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 mr1959 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
vg0702642154 sf0702641155 7 2642154 4.70E-10 2.23E-07
vg0123685482 sf0123684438 1 23685482 6.95E-10 NA
vg1116975625 sf1116509466 11 16975625 7.14E-10 1.23E-06
vg0106770801 sf0106769801 1 6770801 1.40E-09 4.82E-06
vg1116571839 sf1116106717 11 16571839 2.44E-09 3.20E-07
vg0106732078 sf0106731078 1 6732078 3.41E-09 4.01E-06
vg1117544237 sf1117078092 11 17544237 9.66E-08 NA
vg1114490914 sf1114027231 11 14490914 3.78E-07 1.11E-06
vg0519391556 sf0519329040 5 19391556 6.17E-07 NA
vg0105205537 sf0105204537 1 5205537 9.56E-07 NA
vg1001523112 sf1001522089 10 1523112 6.40E-06 4.63E-06
vg1124078257 sf1123612127 11 24078257 NA 8.29E-07