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 mr1929 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
vg0504490188 sf0504490165 5 4490188 2.06E-08 2.06E-08
vg0506467528 sf0506467468 5 6467528 7.15E-08 7.16E-08
vg1017954248 sf1017883020 10 17954248 4.88E-07 4.88E-07
vg0515012929 sf0514955472 5 15012929 5.24E-07 5.24E-07
vg1209285168 sf1209282578 12 9285168 7.55E-07 7.56E-07
vg1215688504 sf1215685801 12 15688504 8.09E-07 8.09E-07
vg0142631029 sf0142629985 1 42631029 8.60E-07 8.60E-07
vg1213685109 sf1213682447 12 13685109 8.91E-07 8.91E-07
vg0729518472 sf0729517480 7 29518472 1.41E-06 1.41E-06
vg0809487809 sf0809486813 8 9487809 1.69E-06 1.69E-06
vg1117573588 sf1117107445 11 17573588 1.88E-06 1.88E-06
vg1225631481 sf1225597876 12 25631481 2.10E-06 2.10E-06
vg0207333714 sf0207333714 2 7333714 2.13E-06 2.13E-06
vg0224343689 sf0224337820 2 24343689 2.92E-06 2.92E-06
vg1213321086 sf1213318424 12 13321086 3.51E-06 3.51E-06
vg0814997105 sf0814994391 8 14997105 3.74E-06 3.74E-06