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 mr1079 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
vg1215869969 sf1215867265 12 15869969 9.55E-45 2.34E-21
vg1211103816 sf1211101182 12 11103816 1.75E-15 NA
vg0218106658 sf0218100789 2 18106658 3.70E-15 7.95E-07
vg1123174932 sf1122708803 11 23174932 3.55E-14 NA
vg1011512136 sf1011440955 10 11512136 3.65E-14 NA
vg1215964459 sf1215961755 12 15964459 NA 1.21E-08
vg1217949602 sf1217921036 12 17949602 NA 1.37E-06
vg0610620315 sf0610619316 6 10620315 NA 3.32E-06
vg0429991723 sf0429806590 4 29991723 NA 3.60E-06
vg0901048761 sf0901047761 9 1048761 NA 3.68E-06
vg1206197673 sf1206196564 12 6197673 NA 4.45E-06