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 mr1996 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
vg0123467869 sf0123466825 1 23467869 7.34E-13 1.97E-06
vg0619445566 sf0619444569 6 19445566 3.07E-12 NA
vg0719339805 sf0719338812 7 19339805 7.22E-12 4.25E-06
vg0223876476 sf0223870607 2 23876476 5.48E-11 NA
vg1126984434 sf1126512821 11 26984434 5.76E-11 NA
vg1126496401 sf1126024815 11 26496401 5.85E-09 8.82E-09
vg1126496390 sf1126024804 11 26496390 3.30E-08 1.71E-08
vg1126497827 sf1126026241 11 26497827 1.96E-07 3.01E-06
vg0300247343 sf0300246343 3 247343 2.50E-07 NA
vg0123335316 sf0123334272 1 23335316 4.66E-07 2.04E-06
vg0123525630 sf0123524586 1 23525630 1.06E-06 NA
vg0714685745 sf0714684752 7 14685745 3.65E-06 NA
vg0811932078 sf0811931083 8 11932078 7.11E-06 2.37E-06
vg0233057746 sf0233051877 2 33057746 NA 3.46E-07
vg0405873164 sf0405868605 4 5873164 NA 3.37E-06
vg1101195615 sf1101194616 11 1195615 NA 4.86E-06
vg1121915235 sf1121449106 11 21915235 NA 8.29E-06