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 mr1080 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
vg0406948359 sf0406943627 4 6948359 5.61E-20 4.56E-11
vg0406944478 sf0406939746 4 6944478 2.65E-18 1.16E-12
vg0406620026 sf0406615470 4 6620026 7.30E-17 1.02E-08
vg0222746228 sf0222740359 2 22746228 1.15E-15 9.07E-08
vg0222721996 sf0222716127 2 22721996 9.59E-15 5.79E-08
vg0222739831 sf0222733962 2 22739831 8.25E-14 1.07E-07
vg1216282260 sf1216279556 12 16282260 7.11E-13 4.82E-06
vg0224620629 sf0224614760 2 24620629 3.56E-12 NA
vg0406529514 sf0406524957 4 6529514 8.98E-12 2.36E-08
vg0618618072 sf0618617075 6 18618072 2.27E-10 2.21E-09
vg0419984850 sf0419812886 4 19984850 1.33E-09 4.54E-08
vg0412144728 sf0412135439 4 12144728 1.58E-09 1.02E-08
vg1216282883 sf1216280179 12 16282883 1.86E-09 1.29E-07
vg0616244147 sf0616243149 6 16244147 4.12E-09 2.17E-09
vg1216930362 sf1216924316 12 16930362 5.15E-09 5.77E-08
vg0205623004 sf0205623004 2 5623004 5.66E-09 NA
vg0613439992 sf0613438993 6 13439992 6.03E-09 1.37E-07
vg0407872167 sf0407867435 4 7872167 1.48E-08 5.75E-11
vg0412484073 sf0412474788 4 12484073 2.12E-08 1.96E-08
vg0412292000 sf0412282715 4 12292000 NA 6.92E-10
vg1215976459 sf1215973755 12 15976459 NA 1.08E-09
vg0222852279 sf0222846410 2 22852279 NA 4.71E-09
vg0400257725 sf0400256725 4 257725 NA 1.82E-08
vg1207742824 sf1207740230 12 7742824 NA 1.98E-08
vg1209644369 sf1209641778 12 9644369 NA 3.10E-08
vg0403617354 sf0403612957 4 3617354 NA 5.62E-08
vg0525534836 sf0525472257 5 25534836 NA 7.48E-08