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 mr1699 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
vg0215430774 sf0215424904 2 15430774 6.99E-43 NA
vg0212265560 sf0212265556 2 12265560 2.28E-42 NA
vg0826168097 sf0826165383 8 26168097 6.14E-41 NA
vg0520453480 sf0520390951 5 20453480 1.77E-40 NA
vg0218350715 sf0218344846 2 18350715 5.57E-39 NA
vg0107074566 sf0107073566 1 7074566 1.08E-36 3.94E-07
vg0331281589 sf0331274474 3 31281589 1.30E-30 3.86E-11
vg0331278847 sf0331271732 3 31278847 1.77E-30 4.53E-11
vg0107081316 sf0107080316 1 7081316 NA 4.08E-15
vg0724526501 sf0724525507 7 24526501 NA 5.66E-12
vg0107072026 sf0107071026 1 7072026 NA 2.74E-11
vg0724501205 sf0724500211 7 24501205 NA 5.41E-11
vg0107062581 sf0107061581 1 7062581 NA 3.69E-10
vg0724436761 sf0724435767 7 24436761 NA 1.32E-09
vg0825021665 sf0825018951 8 25021665 NA 3.26E-09
vg0331256576 sf0331249461 3 31256576 NA 1.44E-08
vg0107084067 sf0107083067 1 7084067 NA 5.03E-08
vg0619498874 sf0619497877 6 19498874 NA 6.57E-08
vg0825196323 sf0825193609 8 25196323 NA 8.90E-08
vg0824848984 sf0824846270 8 24848984 NA 1.66E-07
vg0910053330 sf0910052329 9 10053330 NA 3.97E-07
vg0724465513 sf0724464519 7 24465513 NA 5.17E-07
vg0107111912 sf0107110912 1 7111912 NA 1.01E-06
vg0620619367 sf0620618370 6 20619367 NA 1.43E-06
vg0400676401 sf0400675400 4 676401 NA 1.95E-06
vg0721760874 sf0721759881 7 21760874 NA 2.73E-06
vg0107059016 sf0107058016 1 7059016 NA 3.80E-06