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 mr1588 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
vg1001208884 sf1001207861 10 1208884 1.69E-19 8.53E-17
vg1001211680 sf1001210657 10 1211680 1.53E-18 5.59E-17
vg1001274276 sf1001273253 10 1274276 1.01E-16 4.62E-19
vg1001381368 sf1001380345 10 1381368 3.86E-15 6.37E-27
vg0529552096 sf0529489451 5 29552096 1.94E-14 7.17E-10
vg1001434429 sf1001433406 10 1434429 4.72E-12 5.27E-16
vg0318534639 sf0318533421 3 18534639 8.56E-11 2.27E-08
vg1001244483 sf1001243460 10 1244483 1.53E-10 3.17E-16
vg0403060294 sf0403055898 4 3060294 4.24E-10 6.57E-07
vg1220409045 sf1220380487 12 20409045 3.05E-09 8.53E-07
vg1009451893 sf1009380714 10 9451893 3.36E-09 8.32E-08
vg0412555488 sf0412546198 4 12555488 8.40E-09 1.56E-09
vg1210688076 sf1210685489 12 10688076 2.67E-08 5.06E-07
vg0806818905 sf0806817910 8 6818905 3.36E-08 4.00E-09
vg0406525880 sf0406521323 4 6525880 2.84E-07 3.33E-09
vg1220344311 sf1220315753 12 20344311 3.30E-07 6.83E-06
vg1002107770 sf1002106747 10 2107770 9.98E-07 1.63E-09
vg0808263981 sf0808262985 8 8263981 1.17E-06 1.48E-08
vg1001790923 sf1001789900 10 1790923 1.85E-06 5.52E-10
vg0818608910 sf0818606197 8 18608910 2.46E-06 2.42E-08
vg0821145417 sf0821142704 8 21145417 NA 5.49E-07
vg0211322654 sf0211322651 2 11322654 NA 1.16E-06
vg1001424035 sf1001423012 10 1424035 NA 1.55E-06