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 mr1957 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
vg0225179124 sf0225173255 2 25179124 3.58E-08 2.81E-07
vg0124405284 sf0124404240 1 24405284 7.53E-08 7.84E-07
vg0501809094 sf0501809077 5 1809094 1.36E-07 1.41E-06
vg0502118673 sf0502118647 5 2118673 1.44E-07 4.74E-07
vg0814602612 sf0814599898 8 14602612 1.45E-07 1.69E-06
vg0107825906 sf0107824906 1 7825906 2.84E-07 3.38E-06
vg0124627219 sf0124626175 1 24627219 3.68E-07 1.66E-06
vg0502096444 sf0502096426 5 2096444 4.29E-07 2.11E-07
vg0907970534 sf0907969534 9 7970534 4.32E-07 4.16E-06
vg0911331380 sf0911330379 9 11331380 2.89E-06 9.12E-06