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 mr1042 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
vg1105921472 sf1105917224 11 5921472 1.19E-12 7.24E-06
vg1105907265 sf1105903017 11 5907265 8.66E-12 2.97E-06
vg0431443109 sf0431258007 4 31443109 4.58E-10 NA
vg0114483352 sf0114482326 1 14483352 1.30E-09 NA
vg1219172886 sf1219144356 12 19172886 1.35E-09 NA
vg0431441342 sf0431256240 4 31441342 1.83E-09 NA
vg0131497144 sf0131496100 1 31497144 2.64E-09 NA
vg0413440235 sf0413430949 4 13440235 3.49E-08 2.83E-06
vg0715706128 sf0715705135 7 15706128 1.93E-07 2.88E-06
vg0116735143 sf0116734117 1 16735143 1.33E-06 NA
vg0712504949 sf0712503956 7 12504949 2.07E-06 3.87E-06
vg0141858264 sf0141857221 1 41858264 4.65E-06 NA