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 mr1079 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
vg1215955191 sf1215952487 12 15955191 7.90E-52 1.30E-28
vg1215869969 sf1215867265 12 15869969 4.37E-51 5.50E-25
vg1211103816 sf1211101182 12 11103816 2.08E-16 NA
vg1014467198 sf1014395964 10 14467198 1.59E-15 NA
vg0228377372 sf0228371503 2 28377372 3.32E-15 NA
vg1011512136 sf1011440955 10 11512136 2.55E-14 NA
vg1215964459 sf1215961755 12 15964459 NA 2.02E-10
vg1215970005 sf1215967301 12 15970005 NA 1.81E-09
vg1216482741 sf1216480034 12 16482741 NA 5.36E-08
vg0137184767 sf0137183724 1 37184767 NA 1.32E-07
vg1215211990 sf1215209287 12 15211990 NA 3.71E-07
vg0610620315 sf0610619316 6 10620315 NA 5.58E-07
vg0408293903 sf0408289177 4 8293903 NA 6.54E-07
vg0316036597 sf0316035244 3 16036597 NA 1.61E-06
vg0132377418 sf0132376374 1 32377418 NA 2.48E-06
vg1215903039 sf1215900335 12 15903039 NA 2.50E-06
vg1215271859 sf1215269157 12 15271859 NA 2.99E-06
vg0101639685 sf0101638685 1 1639685 NA 3.96E-06
vg0816078722 sf0816076008 8 16078722 NA 4.53E-06
vg0901555680 sf0901554680 9 1555680 NA 4.72E-06