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 mr1038 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 8.54E-65 4.41E-51
vg1222460913 sf1222427352 12 22460913 7.78E-30 1.72E-18
vg1219585537 sf1219557007 12 19585537 2.31E-21 4.11E-11
vg0303857837 sf0303856833 3 3857837 2.04E-20 5.45E-12
vg1018676755 sf1018605312 10 18676755 3.20E-19 6.35E-09
vg0316797922 sf0316796796 3 16797922 8.20E-18 7.85E-10
vg1016323870 sf1016252646 10 16323870 1.35E-17 1.92E-11
vg1201520069 sf1201519069 12 1520069 8.82E-17 3.27E-08
vg0108515482 sf0108514482 1 8515482 1.33E-16 3.05E-08
vg0226136784 sf0226130915 2 26136784 3.64E-16 2.36E-09
vg0330452376 sf0330445265 3 30452376 1.67E-15 1.34E-08
vg0202925463 sf0202925461 2 2925463 4.29E-15 7.22E-10
vg1117244183 sf1116778035 11 17244183 5.32E-15 3.70E-09
vg0417556620 sf0417384662 4 17556620 1.66E-13 5.86E-09
vg0806359109 sf0806358114 8 6359109 2.81E-13 2.26E-09
vg0728490926 sf0728489934 7 28490926 5.67E-13 2.18E-08
vg0526514954 sf0526452318 5 26514954 2.65E-12 2.55E-08
vg0200045002 sf0200045002 2 45002 3.38E-11 2.84E-08
vg1101299110 sf1101298111 11 1299110 2.64E-09 2.64E-08
vg0406740172 sf0406735618 4 6740172 4.07E-09 1.20E-08
vg0722554916 sf0722553923 7 22554916 1.14E-06 NA