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 mr1374 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
vg0805946030 sf0805945033 8 5946030 5.54E-08 5.54E-08
vg0124420479 sf0124419435 1 24420479 1.25E-07 1.25E-07
vg0321576069 sf0321574579 3 21576069 1.47E-07 1.48E-07
vg0804905723 sf0804904726 8 4905723 3.38E-07 3.38E-07
vg1127480350 sf1127008737 11 27480350 5.67E-07 5.67E-07
vg1020531763 sf1020460242 10 20531763 9.41E-07 9.42E-07
vg0138706549 sf0138705506 1 38706549 9.48E-07 9.48E-07
vg1013182968 sf1013111738 10 13182968 9.52E-07 9.52E-07
vg0218610196 sf0218604327 2 18610196 1.20E-06 1.20E-06
vg0826077942 sf0826075228 8 26077942 1.27E-06 1.27E-06
vg0219780702 sf0219774834 2 19780702 1.67E-06 1.67E-06
vg0500776377 sf0500776359 5 776377 1.94E-06 1.94E-06
vg1001247868 sf1001246845 10 1247868 2.28E-06 2.28E-06
vg0206578247 sf0206578247 2 6578247 2.38E-06 2.38E-06
vg0900843849 sf0900842849 9 843849 2.66E-06 2.66E-06
vg1213065934 sf1213063273 12 13065934 3.28E-06 3.28E-06
vg0610852582 sf0610851583 6 10852582 3.49E-06 3.49E-06
vg0107079035 sf0107078035 1 7079035 4.54E-06 4.54E-06
vg0308543438 sf0308542376 3 8543438 4.57E-06 4.57E-06
vg0113510414 sf0113509388 1 13510414 4.57E-06 4.57E-06