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 mr1280 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
vg1210647989 sf1210645402 12 10647989 8.63E-10 NA
vg0909013229 sf0909012228 9 9013229 4.48E-09 NA
vg0303534207 sf0303533203 3 3534207 5.86E-09 1.14E-06
vg0303605279 sf0303604275 3 3605279 1.73E-08 1.35E-06
vg0110800593 sf0110799569 1 10800593 1.98E-08 NA
vg1217048370 sf1217042324 12 17048370 4.03E-08 NA
vg0826160404 sf0826157690 8 26160404 5.06E-07 3.53E-06
vg1100795910 sf1100794911 11 795910 5.95E-06 2.74E-06
vg0103416626 sf0103415626 1 3416626 9.76E-06 NA
vg0316985667 sf0316984541 3 16985667 NA 1.13E-06
vg0117969733 sf0117968687 1 17969733 NA 2.05E-06
vg0315253958 sf0315252605 3 15253958 NA 2.32E-06
vg0909036057 sf0909035056 9 9036057 NA 4.40E-06