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 mr1284 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
vg0804905723 sf0804904726 8 4905723 8.60E-08 8.60E-08
vg0805946030 sf0805945033 8 5946030 1.28E-07 1.28E-07
vg0805900956 sf0805899959 8 5900956 1.91E-07 1.91E-07
vg0321576069 sf0321574579 3 21576069 2.14E-07 2.14E-07
vg0124420479 sf0124419435 1 24420479 3.80E-07 3.80E-07
vg0206578247 sf0206578247 2 6578247 8.00E-07 8.01E-07
vg0220429795 sf0220423927 2 20429795 1.06E-06 1.06E-06
vg0329703696 sf0329696736 3 29703696 1.22E-06 1.23E-06
vg0826077942 sf0826075228 8 26077942 1.51E-06 1.51E-06
vg1013182968 sf1013111738 10 13182968 1.53E-06 1.53E-06
vg1212024054 sf1212021389 12 12024054 2.09E-06 2.09E-06
vg0138706549 sf0138705506 1 38706549 3.09E-06 3.09E-06
vg0219780702 sf0219774834 2 19780702 3.61E-06 3.61E-06
vg1020531763 sf1020460242 10 20531763 3.67E-06 3.67E-06