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 mr1104 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
vg0719062688 sf0719061695 7 19062688 8.01E-23 2.27E-23
vg0719006525 sf0719005532 7 19006525 1.61E-22 8.40E-24
vg0719039736 sf0719038743 7 19039736 1.44E-17 1.09E-22
vg0107214556 sf0107213556 1 7214556 2.35E-11 5.06E-07
vg0107198487 sf0107197487 1 7198487 8.70E-11 4.92E-08
vg0912061274 sf0912060273 9 12061274 7.03E-10 6.02E-07
vg1217240367 sf1217234322 12 17240367 1.83E-09 6.86E-08
vg0700416280 sf0700415280 7 416280 1.43E-08 2.40E-08
vg0828152822 sf0828150108 8 28152822 2.12E-08 6.57E-08
vg0408294186 sf0408289460 4 8294186 2.64E-08 1.41E-08
vg1101911438 sf1101910439 11 1911438 3.35E-08 1.57E-09
vg0230093704 sf0230087835 2 30093704 1.20E-07 2.69E-07
vg0715273808 sf0715272815 7 15273808 2.96E-07 4.04E-07
vg0113185672 sf0113184646 1 13185672 6.08E-07 1.62E-07
vg0422855440 sf0422670325 4 22855440 6.17E-07 5.77E-07
vg0418074959 sf0417903000 4 18074959 1.65E-06 1.90E-07
vg0413556513 sf0413547227 4 13556513 5.49E-06 2.07E-07
vg0828401472 sf0828398758 8 28401472 6.75E-06 2.36E-10
vg0124736255 sf0124735211 1 24736255 NA 1.32E-08
vg0709019375 sf0709018381 7 9019375 NA 2.30E-07
vg0403478520 sf0403474123 4 3478520 NA 3.19E-07
vg0810519360 sf0810518364 8 10519360 NA 5.43E-07