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 mr1829 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
vg0724515347 sf0724514353 7 24515347 5.46E-28 2.55E-22
vg0724513327 sf0724512333 7 24513327 2.24E-27 6.23E-23
vg0400999452 sf0400995004 4 999452 1.26E-11 6.89E-08
vg0400871651 sf0400870651 4 871651 2.69E-11 2.65E-07
vg1117553288 sf1117087144 11 17553288 5.38E-11 NA
vg0230466138 sf0230460269 2 30466138 7.11E-11 9.80E-07
vg0724504126 sf0724503132 7 24504126 1.48E-10 2.06E-07
vg0725312091 sf0725311097 7 25312091 2.00E-10 5.08E-09
vg1210687991 sf1210685404 12 10687991 6.41E-10 8.58E-08
vg0106770885 sf0106769885 1 6770885 9.58E-09 1.32E-06
vg0621705457 sf0621704460 6 21705457 2.79E-07 1.38E-06
vg0721876471 sf0721875478 7 21876471 3.47E-06 1.40E-07
vg0200600738 sf0200600738 2 600738 5.52E-06 8.26E-06
vg0712392714 sf0712391721 7 12392714 6.05E-06 9.90E-07
vg0724487049 sf0724486055 7 24487049 NA 2.26E-12
vg0233123079 sf0233117210 2 33123079 NA 3.16E-07
vg1119375381 sf1118909069 11 19375381 NA 4.18E-07
vg0404711278 sf0404706717 4 4711278 NA 1.08E-06
vg0618477957 sf0618476960 6 18477957 NA 4.98E-06