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 mr1653 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
vg0205720488 sf0205720488 2 5720488 2.16E-21 4.09E-07
vg1105668680 sf1105664432 11 5668680 6.28E-19 NA
vg0427290211 sf0427105080 4 27290211 1.80E-18 NA
vg0321208630 sf0321207140 3 21208630 2.61E-18 NA
vg0808906949 sf0808905953 8 8906949 1.23E-17 NA
vg0630642055 sf0630641057 6 30642055 1.57E-17 1.12E-06
vg0630658313 sf0630657315 6 30658313 5.01E-17 9.56E-07
vg1204011153 sf1204010141 12 4011153 NA 6.12E-06