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 mr1033 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
vg0612828976 sf0612827977 6 12828976 2.49E-14 1.87E-09
vg0613153084 sf0613152085 6 13153084 7.75E-14 1.62E-08
vg0613389030 sf0613388031 6 13389030 6.08E-13 2.18E-07
vg0613381040 sf0613380041 6 13381040 1.61E-12 9.97E-09
vg0617850077 sf0617849080 6 17850077 3.85E-12 2.51E-06
vg0618534600 sf0618533603 6 18534600 4.68E-12 3.06E-08
vg0617614534 sf0617613537 6 17614534 7.63E-12 1.51E-06
vg0619639208 sf0619638211 6 19639208 1.01E-11 1.56E-07
vg0613550511 sf0613549512 6 13550511 2.31E-11 2.19E-07
vg0624489994 sf0624488997 6 24489994 3.99E-11 NA
vg0613550053 sf0613549054 6 13550053 4.90E-11 2.50E-06
vg0613624979 sf0613623980 6 13624979 6.29E-11 1.79E-06
vg0612016577 sf0612015578 6 12016577 2.50E-10 6.82E-07
vg0619711521 sf0619710524 6 19711521 3.86E-10 2.16E-06
vg0613374729 sf0613373730 6 13374729 5.64E-10 3.14E-06
vg0315290362 sf0315289009 3 15290362 7.32E-10 1.62E-07
vg0617811733 sf0617810736 6 17811733 3.18E-09 2.45E-06
vg0226057933 sf0226052064 2 26057933 3.39E-08 5.05E-10
vg0216120581 sf0216114711 2 16120581 4.75E-08 3.00E-07
vg0617623173 sf0617622176 6 17623173 1.66E-07 3.31E-07
vg1109136047 sf1109130626 11 9136047 NA 1.44E-06
vg0717214532 sf0717213539 7 17214532 NA 2.06E-06
vg1104422108 sf1104418010 11 4422108 NA 2.91E-06