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 mr1241 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
vg0707666300 sf0707665305 7 7666300 4.27E-11 NA
vg1201739740 sf1201738737 12 1739740 1.39E-10 NA
vg0230660705 sf0230654836 2 30660705 2.43E-10 NA
vg0707876376 sf0707875381 7 7876376 3.47E-10 NA
vg0305015386 sf0305014388 3 5015386 3.58E-10 NA
vg1201512648 sf1201511648 12 1512648 6.02E-10 4.80E-06
vg0719133785 sf0719132792 7 19133785 7.52E-10 2.71E-06
vg1202102394 sf1202101392 12 2102394 1.52E-09 1.23E-06
vg0429423704 sf0429233786 4 29423704 6.57E-09 4.76E-06
vg0719007567 sf0719006574 7 19007567 NA 4.53E-06
vg1205521566 sf1205520552 12 5521566 NA 4.75E-06
vg0428010540 sf0427825404 4 28010540 NA 6.64E-06