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 mr1677 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
vg0101292923 sf0101291923 1 1292923 2.35E-08 NA
vg0506748703 sf0506748645 5 6748703 2.82E-08 5.61E-06
vg0223719895 sf0223714026 2 23719895 4.66E-08 NA
vg0140816254 sf0140815211 1 40816254 4.94E-08 NA
vg0423143043 sf0422957898 4 23143043 5.65E-08 NA
vg0506744833 sf0506744775 5 6744833 1.01E-07 2.59E-06
vg0131503760 sf0131502716 1 31503760 2.87E-07 1.41E-06
vg0114208243 sf0114207217 1 14208243 2.60E-06 6.55E-06
vg0715381494 sf0715380501 7 15381494 4.16E-06 NA
vg0329975862 sf0329968901 3 29975862 NA 3.11E-06
vg1216401476 sf1216398769 12 16401476 NA 3.38E-06