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 mr1742 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
vg1116062677 sf1115597549 11 16062677 1.90E-11 1.02E-07
vg1107589818 sf1107585563 11 7589818 6.06E-11 2.68E-07
vg0330722786 sf0330715673 3 30722786 1.56E-10 3.55E-07
vg1227454410 sf1227420810 12 27454410 5.75E-10 1.94E-06
vg0303943543 sf0303942539 3 3943543 5.77E-10 6.39E-07
vg0706300847 sf0706299850 7 6300847 1.32E-09 3.17E-06
vg0141963550 sf0141962507 1 41963550 6.28E-08 2.66E-06
vg0306113744 sf0306112744 3 6113744 1.28E-06 NA
vg0703855509 sf0703854510 7 3855509 7.64E-06 NA
vg1114404010 sf1113940327 11 14404010 NA 1.19E-06
vg0815520975 sf0815518261 8 15520975 NA 3.90E-06