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 mr1790 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
vg0228495434 sf0228489565 2 28495434 2.02E-18 NA
vg0526075747 sf0526013167 5 26075747 7.32E-18 NA
vg0112658603 sf0112657577 1 12658603 1.20E-17 NA
vg1224662551 sf1224629005 12 24662551 2.09E-17 NA
vg0402172640 sf0402168235 4 2172640 2.39E-17 NA
vg0431162265 sf0430977156 4 31162265 NA 8.23E-08
vg1124648589 sf1124182429 11 24648589 NA 2.08E-07
vg0421497689 sf0421325740 4 21497689 NA 5.21E-07
vg0225187660 sf0225181791 2 25187660 NA 8.54E-07
vg0525567832 sf0525505253 5 25567832 NA 1.93E-06
vg1128025024 sf1127553410 11 28025024 NA 4.74E-06
vg0918880163 sf0918879163 9 18880163 NA 7.06E-06