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 mr1159 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 1.56E-08 1.56E-08
vg0124420479 sf0124419435 1 24420479 2.66E-08 2.67E-08
vg0321576069 sf0321574579 3 21576069 2.92E-08 2.93E-08
vg0329703696 sf0329696736 3 29703696 4.44E-08 4.44E-08
vg1013182968 sf1013111738 10 13182968 4.85E-08 4.85E-08
vg0714142381 sf0714141388 7 14142381 5.06E-08 5.06E-08
vg0804905723 sf0804904726 8 4905723 6.20E-08 6.20E-08
vg0218610196 sf0218604327 2 18610196 2.05E-07 2.05E-07
vg0509233251 sf0509233180 5 9233251 2.62E-07 2.62E-07
vg0706732811 sf0706731816 7 6732811 3.01E-07 3.01E-07
vg0205924397 sf0205924397 2 5924397 3.08E-07 3.08E-07
vg1001247868 sf1001246845 10 1247868 3.83E-07 3.83E-07
vg0138706549 sf0138705506 1 38706549 3.88E-07 3.89E-07
vg0714140419 sf0714139426 7 14140419 4.33E-07 4.33E-07
vg0505860625 sf0505860563 5 5860625 4.53E-07 4.54E-07
vg0317372993 sf0317371803 3 17372993 5.89E-07 5.89E-07
vg0107079035 sf0107078035 1 7079035 6.64E-07 6.64E-07
vg0826077942 sf0826075228 8 26077942 7.51E-07 7.51E-07
vg1212024054 sf1212021389 12 12024054 8.44E-07 8.45E-07
vg0900843849 sf0900842849 9 843849 8.70E-07 8.70E-07