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 mr1687 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
vg0124420479 sf0124419435 1 24420479 1.67E-08 1.67E-08
vg0805900956 sf0805899959 8 5900956 3.48E-08 3.48E-08
vg0900843849 sf0900842849 9 843849 2.07E-07 2.07E-07
vg0138706549 sf0138705506 1 38706549 2.93E-07 2.93E-07
vg0222002131 sf0221996262 2 22002131 5.78E-07 5.78E-07
vg1013182968 sf1013111738 10 13182968 6.66E-07 6.67E-07
vg0509233251 sf0509233180 5 9233251 7.78E-07 7.78E-07
vg0804905723 sf0804904726 8 4905723 9.59E-07 9.60E-07
vg0321576069 sf0321574579 3 21576069 1.29E-06 1.29E-06
vg0329703696 sf0329696736 3 29703696 1.80E-06 1.80E-06
vg0805055173 sf0805054176 8 5055173 2.16E-06 2.16E-06
vg0500776377 sf0500776359 5 776377 2.49E-06 2.49E-06
vg0606109335 sf0606108336 6 6109335 3.00E-06 3.01E-06
vg0206301209 sf0206301209 2 6301209 3.42E-06 3.42E-06
vg0826077942 sf0826075228 8 26077942 3.66E-06 3.66E-06
vg1001247868 sf1001246845 10 1247868 3.81E-06 3.81E-06
vg1118023722 sf1117557580 11 18023722 4.97E-06 4.97E-06