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 mr1063 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
vg1125567949 sf1125101788 11 25567949 8.65E-12 6.60E-06
vg1125679207 sf1125213046 11 25679207 3.69E-11 NA
vg0601213318 sf0601212319 6 1213318 5.53E-11 7.19E-06
vg0706245344 sf0706244345 7 6245344 1.48E-10 NA
vg0805577197 sf0805576200 8 5577197 4.74E-10 NA
vg0600688589 sf0600687590 6 688589 1.60E-09 4.02E-08
vg0713261979 sf0713260986 7 13261979 5.20E-08 NA
vg0317031987 sf0317030861 3 17031987 5.91E-07 3.16E-06
vg0224592440 sf0224586571 2 24592440 5.13E-06 NA
vg0412619214 sf0412609924 4 12619214 6.18E-06 4.78E-06
vg0222739831 sf0222733962 2 22739831 9.21E-06 4.99E-06
vg0802219948 sf0802218951 8 2219948 NA 2.68E-06