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 mr1278 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 2.74E-08 2.74E-08
vg1127480350 sf1127008737 11 27480350 4.82E-07 4.82E-07
vg0124420479 sf0124419435 1 24420479 4.88E-07 4.88E-07
vg0805005643 sf0805004646 8 5005643 6.34E-07 6.34E-07
vg0329703696 sf0329696736 3 29703696 6.84E-07 6.84E-07
vg0826077942 sf0826075228 8 26077942 7.29E-07 7.29E-07
vg1013182968 sf1013111738 10 13182968 8.98E-07 8.98E-07
vg0219780702 sf0219774834 2 19780702 1.08E-06 1.08E-06
vg0138706549 sf0138705506 1 38706549 1.45E-06 1.45E-06
vg0107079035 sf0107078035 1 7079035 1.68E-06 1.68E-06
vg1212024054 sf1212021389 12 12024054 2.26E-06 2.26E-06
vg0218610196 sf0218604327 2 18610196 3.64E-06 3.64E-06
vg0500776377 sf0500776359 5 776377 4.21E-06 4.21E-06
vg1020531763 sf1020460242 10 20531763 4.34E-06 4.34E-06
vg0900843849 sf0900842849 9 843849 4.56E-06 4.56E-06