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 mr1113 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
vg0421391589 sf0421219642 4 21391589 2.47E-11 3.20E-09
vg0421387824 sf0421215877 4 21387824 3.70E-11 1.59E-09
vg1117137503 sf1116671355 11 17137503 1.71E-10 8.02E-10
vg0915298743 sf0915297742 9 15298743 3.81E-10 6.43E-08
vg1115861799 sf1115397090 11 15861799 5.27E-10 5.22E-08
vg0103158009 sf0103157009 1 3158009 1.02E-09 4.04E-07
vg0700863821 sf0700862821 7 863821 1.26E-08 5.71E-07
vg0913444404 sf0913443403 9 13444404 1.27E-08 2.49E-07
vg1125101682 sf1124635522 11 25101682 1.54E-08 8.93E-07
vg0108582948 sf0108581948 1 8582948 2.26E-08 3.01E-06
vg0432663252 sf0432478141 4 32663252 2.50E-08 1.64E-06
vg0709675216 sf0709674222 7 9675216 3.11E-08 7.02E-07
vg1201867679 sf1201866676 12 1867679 5.59E-08 9.33E-07
vg0728000317 sf0727999324 7 28000317 7.67E-08 2.09E-06
vg0136299082 sf0136298039 1 36299082 8.02E-08 6.80E-07
vg0630599588 sf0630598590 6 30599588 1.23E-07 3.74E-07
vg0133764184 sf0133763140 1 33764184 2.10E-07 1.08E-07
vg0432345183 sf0432160072 4 32345183 2.20E-07 2.02E-07
vg0107057661 sf0107056661 1 7057661 2.68E-07 6.27E-07
vg1122441548 sf1121975419 11 22441548 9.66E-07 1.46E-06
vg0224215161 sf0224209292 2 24215161 1.28E-06 2.97E-07
vg0223848979 sf0223843110 2 23848979 NA 1.57E-06