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 mr1961 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
vg0222679274 sf0222673405 2 22679274 4.67E-28 2.67E-11
vg0222675535 sf0222669666 2 22675535 4.55E-26 1.45E-11
vg0100375558 sf0100374558 1 375558 3.25E-22 7.64E-06
vg1221253318 sf1221219864 12 21253318 4.51E-22 NA
vg0100356236 sf0100355236 1 356236 9.26E-22 8.59E-07
vg1006242803 sf1006258426 10 6242803 3.47E-21 5.06E-06
vg0818212763 sf0818210050 8 18212763 3.86E-21 7.53E-06
vg1110425815 sf1110420360 11 10425815 5.33E-19 3.19E-06
vg1009142714 sf1009071575 10 9142714 3.53E-15 2.56E-06
vg0222741463 sf0222735594 2 22741463 NA 9.16E-08
vg0140883886 sf0140882843 1 40883886 NA 9.40E-08
vg0224791200 sf0224785331 2 24791200 NA 2.96E-07
vg1004721424 sf1004737961 10 4721424 NA 4.95E-07
vg1016225510 sf1016154282 10 16225510 NA 5.37E-07
vg1009514604 sf1009443425 10 9514604 NA 1.46E-06
vg1209218924 sf1209216333 12 9218924 NA 2.19E-06
vg1016310858 sf1016239634 10 16310858 NA 2.60E-06
vg0315165022 sf0315163669 3 15165022 NA 2.68E-06
vg0805024489 sf0805023492 8 5024489 NA 3.13E-06
vg0316092122 sf0316090769 3 16092122 NA 3.79E-06
vg1005950387 sf1005966925 10 5950387 NA 3.88E-06
vg0315922266 sf0315920913 3 15922266 NA 4.21E-06
vg0205946715 sf0205946715 2 5946715 NA 8.87E-06