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 mr1620 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
vg0719039736 sf0719038743 7 19039736 3.42E-21 4.25E-19
vg0820065663 sf0820062950 8 20065663 1.12E-08 2.18E-06
vg0230189175 sf0230183306 2 30189175 4.22E-08 NA
vg0725004532 sf0725003538 7 25004532 9.20E-08 9.69E-07
vg0413556513 sf0413547227 4 13556513 2.40E-07 1.91E-06
vg1007607743 sf1007623352 10 7607743 2.55E-07 9.25E-07
vg0230093704 sf0230087835 2 30093704 7.00E-07 3.77E-06
vg0422772120 sf0422587003 4 22772120 7.32E-07 1.51E-06
vg0419763927 sf0419591962 4 19763927 5.07E-06 2.23E-06
vg0719053396 sf0719052403 7 19053396 8.29E-06 1.65E-09