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 mr1718 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
vg0319434107 sf0319432618 3 19434107 2.74E-19 1.52E-14
vg0322035566 sf0322034073 3 22035566 8.44E-18 2.15E-13
vg0319043512 sf0319042272 3 19043512 3.39E-12 7.64E-07
vg1214622453 sf1214619793 12 14622453 4.40E-12 7.37E-10
vg0318448002 sf0318446784 3 18448002 7.89E-12 1.50E-06
vg0318193307 sf0318192089 3 18193307 1.18E-11 6.02E-07
vg0319079517 sf0319078277 3 19079517 1.94E-11 3.06E-07
vg0319801567 sf0319800078 3 19801567 3.53E-11 1.48E-07
vg0318242759 sf0318241541 3 18242759 3.92E-11 8.51E-07
vg0322461073 sf0322459562 3 22461073 4.71E-11 4.18E-07
vg1214622278 sf1214619618 12 14622278 1.20E-10 4.87E-10
vg0320629521 sf0320628031 3 20629521 2.43E-10 6.08E-07
vg0318241664 sf0318240446 3 18241664 4.22E-10 1.77E-07
vg0321218309 sf0321216819 3 21218309 4.71E-10 1.42E-06
vg0321733880 sf0321732390 3 21733880 8.30E-10 NA
vg0320863559 sf0320862069 3 20863559 9.52E-10 1.65E-06
vg0320639721 sf0320638231 3 20639721 2.18E-09 1.12E-06
vg0317492428 sf0317491210 3 17492428 3.02E-09 8.78E-07
vg0808428262 sf0808427266 8 8428262 5.78E-09 9.46E-07
vg1215882208 sf1215879504 12 15882208 1.33E-08 1.26E-06
vg1215678000 sf1215675297 12 15678000 3.71E-07 NA
vg1003769168 sf1003768144 10 3769168 1.48E-06 1.87E-07
vg1010576786 sf1010505607 10 10576786 NA 4.95E-07
vg0118083761 sf0118082715 1 18083761 NA 1.27E-06