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 mr1389 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
vg0729105428 sf0729104436 7 29105428 1.07E-85 1.02E-68
vg1222460913 sf1222427352 12 22460913 4.32E-33 2.99E-20
vg1219585537 sf1219557007 12 19585537 4.95E-25 1.09E-12
vg0303857837 sf0303856833 3 3857837 7.76E-23 1.17E-12
vg0316797922 sf0316796796 3 16797922 4.96E-22 4.98E-12
vg0333009355 sf0333002225 3 33009355 1.34E-21 9.78E-10
vg0219834070 sf0219828202 2 19834070 4.56E-21 3.09E-11
vg1201520069 sf1201519069 12 1520069 7.05E-20 1.49E-09
vg0226136784 sf0226130915 2 26136784 5.86E-18 1.33E-09
vg1117244183 sf1116778035 11 17244183 6.19E-18 3.40E-11
vg0330452376 sf0330445265 3 30452376 8.44E-18 3.46E-10
vg1016323870 sf1016252646 10 16323870 1.99E-17 9.18E-10
vg0726950185 sf0726949191 7 26950185 3.83E-16 6.00E-10
vg0417556620 sf0417384662 4 17556620 2.17E-15 6.29E-11
vg0202925463 sf0202925461 2 2925463 2.68E-15 2.12E-09
vg0200045002 sf0200045002 2 45002 4.69E-14 4.22E-11
vg0806359109 sf0806358114 8 6359109 9.89E-13 2.47E-09
vg0728689079 sf0728688087 7 28689079 6.06E-12 1.05E-09
vg1207361973 sf1207359380 12 7361973 2.13E-11 1.31E-09
vg1101299110 sf1101298111 11 1299110 2.83E-11 1.13E-10
vg0220834541 sf0220828673 2 20834541 1.78E-08 NA