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 mr1307 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
vg0230674592 sf0230668723 2 30674592 3.35E-14 NA
vg0328103024 sf0328096078 3 28103024 4.25E-14 NA
vg0825302529 sf0825299815 8 25302529 7.33E-14 5.44E-06
vg0316974733 sf0316973607 3 16974733 1.13E-13 NA
vg0922501220 sf0922500739 9 22501220 1.32E-13 NA
vg0910187686 sf0910186685 9 10187686 1.15E-12 1.96E-06
vg0422542724 sf0422357611 4 22542724 4.55E-12 4.31E-06
vg1128648694 sf1128125473 11 28648694 NA 3.68E-06
vg0714379547 sf0714378554 7 14379547 NA 6.60E-06