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 mr1204 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
vg1004296464 sf1004313002 10 4296464 3.23E-11 1.26E-07
vg1104978749 sf1104974560 11 4978749 4.15E-11 2.06E-06
vg1104978881 sf1104974692 11 4978881 1.09E-10 1.08E-06
vg0130623883 sf0130622839 1 30623883 3.51E-10 NA
vg0416878791 sf0416706833 4 16878791 7.79E-10 7.29E-06
vg0610002564 sf0610001565 6 10002564 1.77E-09 5.53E-06
vg0121871143 sf0121870098 1 21871143 1.12E-07 2.13E-06
vg1210553397 sf1210550810 12 10553397 3.99E-07 NA
vg0820888052 sf0820885339 8 20888052 4.91E-07 NA
vg1009412063 sf1009340884 10 9412063 5.59E-06 3.24E-06
vg0805469573 sf0805468576 8 5469573 7.56E-06 4.83E-07
vg0412457585 sf0412448300 4 12457585 7.69E-06 4.88E-06
vg1105377831 sf1105373582 11 5377831 NA 4.53E-06