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 mr1641 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
vg0205285978 sf0205285976 2 5285978 3.10E-27 6.69E-12
vg0232480149 sf0232474280 2 32480149 2.61E-17 5.81E-06
vg0138523638 sf0138522595 1 38523638 4.64E-17 NA
vg0306258301 sf0306257301 3 6258301 5.29E-17 NA
vg0232479992 sf0232474123 2 32479992 7.59E-17 4.81E-06
vg0727110534 sf0727109540 7 27110534 2.38E-16 9.97E-06
vg0805964617 sf0805963620 8 5964617 1.05E-13 6.38E-07
vg0335297514 sf0335290383 3 35297514 9.79E-13 1.80E-06
vg0528836237 sf0528773592 5 28836237 1.13E-12 4.04E-06
vg1214662996 sf1214660336 12 14662996 2.66E-12 2.14E-07
vg0805992743 sf0805991746 8 5992743 NA 4.41E-07
vg0419224532 sf0419052570 4 19224532 NA 7.85E-07
vg0607961607 sf0607960608 6 7961607 NA 1.23E-06
vg0133432014 sf0133430970 1 33432014 NA 1.68E-06
vg1118023722 sf1117557580 11 18023722 NA 1.92E-06
vg1007863061 sf1007878671 10 7863061 NA 2.00E-06
vg0805944879 sf0805943882 8 5944879 NA 2.11E-06
vg0205293173 sf0205293171 2 5293173 NA 3.98E-06