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 mr1663 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
vg0321576069 sf0321574579 3 21576069 2.68E-10 2.68E-10
vg0805946030 sf0805945033 8 5946030 6.18E-10 6.18E-10
vg0124420479 sf0124419435 1 24420479 1.96E-09 1.96E-09
vg0826077942 sf0826075228 8 26077942 2.34E-08 2.34E-08
vg0329703696 sf0329696736 3 29703696 2.93E-08 2.93E-08
vg1013182968 sf1013111738 10 13182968 5.90E-08 5.90E-08
vg0107079035 sf0107078035 1 7079035 9.04E-08 9.04E-08
vg0113510414 sf0113509388 1 13510414 9.30E-08 9.30E-08
vg0804905723 sf0804904726 8 4905723 1.07E-07 1.07E-07
vg0629600574 sf0629599576 6 29600574 2.70E-07 2.70E-07
vg0138706549 sf0138705506 1 38706549 4.27E-07 4.27E-07
vg0500776377 sf0500776359 5 776377 5.22E-07 5.22E-07
vg0610852582 sf0610851583 6 10852582 6.18E-07 6.18E-07
vg0206578247 sf0206578247 2 6578247 6.70E-07 6.70E-07
vg0414587628 sf0414578342 4 14587628 7.20E-07 7.20E-07
vg0606109335 sf0606108336 6 6109335 8.47E-07 8.48E-07
vg0218569230 sf0218563361 2 18569230 9.17E-07 9.18E-07
vg0630441706 sf0630440708 6 30441706 9.42E-07 9.42E-07
vg0205924397 sf0205924397 2 5924397 1.84E-06 1.84E-06
vg0808428148 sf0808427152 8 8428148 1.91E-06 1.91E-06
vg1001247868 sf1001246845 10 1247868 3.33E-06 3.33E-06