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 mr1745 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
vg0430559445 sf0430374320 4 30559445 2.97E-34 1.13E-25
vg0430616892 sf0430431767 4 30616892 6.93E-15 2.05E-10
vg0430572046 sf0430386921 4 30572046 1.74E-13 3.16E-11
vg0325946462 sf0325944478 3 25946462 1.38E-12 NA
vg1127119606 sf1126647993 11 27119606 1.65E-11 3.11E-07
vg0430792799 sf0430607672 4 30792799 3.08E-11 NA
vg0427340146 sf0427155012 4 27340146 1.47E-08 4.48E-09
vg0225876283 sf0225870414 2 25876283 2.15E-07 1.19E-06
vg0702899416 sf0702898417 7 2899416 3.11E-07 1.04E-06
vg0430744499 sf0430559371 4 30744499 2.86E-06 2.75E-06
vg0430855895 sf0430670775 4 30855895 4.03E-06 8.86E-09
vg0519461555 sf0519399039 5 19461555 NA 1.12E-06
vg0709326055 sf0709325061 7 9326055 NA 2.47E-06
vg1220916154 sf1220882703 12 20916154 NA 4.98E-06