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 mr1536 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
vg0613480388 sf0613479389 6 13480388 1.04E-108 6.68E-14
vg0619553148 sf0619552151 6 19553148 2.96E-106 2.86E-06
vg0616387632 sf0616386634 6 16387632 7.22E-105 2.62E-07
vg0133296080 sf0133295036 1 33296080 2.11E-100 NA
vg0304913055 sf0304912057 3 4913055 1.28E-99 NA
vg0613473372 sf0613472373 6 13473372 3.74E-98 1.58E-14
vg0618101294 sf0618100297 6 18101294 1.00E-96 2.13E-12
vg0133601653 sf0133600609 1 33601653 2.88E-95 4.64E-09
vg0620862658 sf0620861661 6 20862658 1.44E-93 1.81E-07
vg0921453243 sf0921452762 9 21453243 NA 1.53E-11
vg0921421309 sf0921420828 9 21421309 NA 3.70E-11
vg0921523713 sf0921523232 9 21523713 NA 6.51E-09
vg0133363407 sf0133362363 1 33363407 NA 3.67E-08
vg0613465771 sf0613464772 6 13465771 NA 4.14E-08
vg0918181871 sf0918180870 9 18181871 NA 7.84E-07
vg1215403123 sf1215400421 12 15403123 NA 1.03E-06