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 mr1542 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
vg1209876216 sf1209873626 12 9876216 1.37E-11 1.37E-11
vg1219817262 sf1219788732 12 19817262 2.03E-08 2.03E-08
vg0722262097 sf0722261104 7 22262097 7.05E-08 7.05E-08
vg0611318612 sf0611317613 6 11318612 1.58E-07 1.58E-07
vg1003385190 sf1003384167 10 3385190 2.15E-07 2.15E-07
vg0809154270 sf0809153274 8 9154270 3.83E-07 3.83E-07
vg0433192266 sf0433007154 4 33192266 4.42E-07 4.42E-07
vg0618969985 sf0618968988 6 18969985 9.22E-07 9.22E-07
vg1020721566 sf1020650045 10 20721566 1.18E-06 1.18E-06
vg1016998464 sf1016927236 10 16998464 1.60E-06 1.60E-06
vg0600569739 sf0600568740 6 569739 2.01E-06 2.01E-06
vg0431857188 sf0431672082 4 31857188 3.25E-06 3.25E-06
vg0619658716 sf0619657719 6 19658716 3.45E-06 3.45E-06
vg0710881399 sf0710880405 7 10881399 3.74E-06 3.74E-06