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 mr1383 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
vg0700118960 sf0700117960 7 118960 2.52E-17 1.09E-09
vg0104860223 sf0104859223 1 4860223 5.03E-13 2.76E-06
vg0702869915 sf0702868916 7 2869915 7.90E-12 NA
vg0104668106 sf0104667106 1 4668106 4.62E-11 NA
vg1102801424 sf1102797328 11 2801424 8.19E-11 NA
vg0819439793 sf0819437080 8 19439793 1.02E-08 1.30E-06
vg0119738433 sf0119737388 1 19738433 NA 3.41E-07
vg1000328907 sf1000327907 10 328907 NA 4.61E-07
vg1200851947 sf1200850947 12 851947 NA 4.15E-06
vg0114889993 sf0114888967 1 14889993 NA 4.23E-06
vg0114890522 sf0114889496 1 14890522 NA 8.10E-06