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 mr1949 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
vg0719316520 sf0719315527 7 19316520 1.55E-18 3.40E-14
vg0719300893 sf0719299900 7 19300893 2.10E-18 4.72E-15
vg0719052876 sf0719051883 7 19052876 5.95E-11 1.25E-06
vg0719140447 sf0719139454 7 19140447 6.01E-11 7.36E-07
vg0719140489 sf0719139496 7 19140489 1.11E-10 4.76E-07
vg0719123523 sf0719122530 7 19123523 2.38E-10 1.97E-06
vg0417644545 sf0417472586 4 17644545 5.19E-10 3.44E-06
vg1201804345 sf1201803342 12 1804345 3.49E-09 NA
vg0228211032 sf0228205163 2 28211032 4.40E-09 3.96E-06
vg0717197101 sf0717196108 7 17197101 7.62E-09 2.69E-06
vg0323102859 sf0323101347 3 23102859 1.88E-08 6.75E-07
vg0336362940 sf0336355810 3 36362940 2.13E-08 5.98E-09
vg0432427528 sf0432242419 4 32427528 2.62E-08 3.51E-06
vg0719466349 sf0719465356 7 19466349 4.28E-08 1.42E-06
vg0718983676 sf0718982683 7 18983676 5.27E-08 1.63E-08
vg0504429178 sf0504429155 5 4429178 5.61E-07 NA
vg0335957254 sf0335950123 3 35957254 1.22E-06 NA
vg0206102808 sf0206102808 2 6102808 4.74E-06 1.70E-06
vg0431597089 sf0431411984 4 31597089 8.23E-06 NA
vg0717328894 sf0717327901 7 17328894 NA 2.68E-06
vg0826333758 sf0826331044 8 26333758 NA 3.46E-06
vg1220176033 sf1220147475 12 20176033 NA 3.93E-06
vg0810831297 sf0810830302 8 10831297 NA 4.73E-06