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 8.33E-107 1.22E-89
vg1222460913 sf1222427352 12 22460913 9.57E-37 2.35E-24
vg1219585537 sf1219557007 12 19585537 2.30E-29 6.13E-17
vg1107793749 sf1107789494 11 7793749 1.29E-23 3.32E-09
vg0328706766 sf0328699820 3 28706766 1.01E-21 3.44E-09
vg0303857837 sf0303856833 3 3857837 1.88E-21 9.83E-11
vg1201520069 sf1201519069 12 1520069 3.87E-21 1.08E-09
vg0108515482 sf0108514482 1 8515482 8.22E-21 1.88E-11
vg0417556620 sf0417384662 4 17556620 4.26E-20 9.04E-15
vg0316797922 sf0316796796 3 16797922 2.46E-19 5.16E-10
vg1221198057 sf1221164603 12 21198057 8.52E-19 9.24E-14
vg0219834070 sf0219828202 2 19834070 1.15E-18 7.24E-11
vg0228423420 sf0228417551 2 28423420 6.32E-17 7.05E-11
vg0726950185 sf0726949191 7 26950185 7.52E-17 6.49E-12
vg0325722534 sf0325720552 3 25722534 8.91E-16 3.49E-10
vg1016323870 sf1016252646 10 16323870 1.32E-15 8.48E-10
vg0522027089 sf0521964531 5 22027089 4.00E-15 8.50E-10
vg0616470948 sf0616469950 6 16470948 1.57E-14 2.35E-09
vg0728689079 sf0728688087 7 28689079 5.31E-14 1.54E-10
vg1223507277 sf1223473737 12 23507277 1.37E-11 1.77E-09
vg0401713889 sf0401709438 4 1713889 2.09E-11 3.61E-10
vg1101299110 sf1101298111 11 1299110 1.57E-09 1.70E-09
vg0304762695 sf0304761697 3 4762695 3.45E-08 3.06E-10
vg1112955270 sf1112491591 11 12955270 2.00E-06 1.45E-06