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 mr1768 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
vg1005366897 sf1005383434 10 5366897 5.80E-12 1.30E-06
vg1005442522 sf1005459059 10 5442522 1.20E-10 4.83E-07
vg1010268867 sf1010197688 10 10268867 4.96E-09 NA
vg1004230664 sf1004247202 10 4230664 5.84E-09 9.16E-08
vg1110630869 sf1110625414 11 10630869 1.95E-08 NA
vg1004245904 sf1004262442 10 4245904 2.36E-08 9.27E-07
vg0420827862 sf0420655905 4 20827862 5.62E-08 NA
vg0423532668 sf0423347525 4 23532668 3.12E-07 8.37E-07
vg0420830218 sf0420658261 4 20830218 6.13E-07 NA
vg0526099235 sf0526036655 5 26099235 7.81E-07 NA
vg0911164560 sf0911163559 9 11164560 1.93E-06 4.28E-06
vg1002869131 sf1002868108 10 2869131 2.45E-06 2.84E-07