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 mr1293 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
vg1227186466 sf1227152866 12 27186466 4.98E-09 NA
vg0220342715 sf0220336847 2 20342715 5.74E-09 8.08E-07
vg1216110511 sf1216107807 12 16110511 1.03E-08 6.22E-06
vg0305129097 sf0305128099 3 5129097 1.98E-08 NA
vg1103050384 sf1103046288 11 3050384 2.69E-08 NA
vg1126312813 sf1125841226 11 26312813 5.37E-08 9.73E-06
vg0434768134 sf0434583025 4 34768134 4.92E-07 3.54E-07
vg1213065934 sf1213063273 12 13065934 7.44E-07 NA
vg1219176479 sf1219147949 12 19176479 7.68E-06 4.08E-06
vg0524262516 sf0524199935 5 24262516 8.60E-06 NA
vg0232481318 sf0232475449 2 32481318 NA 3.88E-06