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 mr1141 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
vg0602403184 sf0602402185 6 2403184 2.30E-46 9.60E-22
vg0602811391 sf0602810392 6 2811391 3.75E-45 1.25E-23
vg0729105428 sf0729104436 7 29105428 3.09E-20 5.89E-19
vg0602936123 sf0602935124 6 2936123 8.12E-16 NA
vg0601660746 sf0601659747 6 1660746 4.24E-15 1.58E-06
vg0604336913 sf0604335914 6 4336913 2.30E-14 NA
vg1222460913 sf1222427352 12 22460913 7.69E-14 2.02E-11
vg0601347422 sf0601346423 6 1347422 2.58E-13 1.13E-06
vg1018676755 sf1018605312 10 18676755 1.23E-12 2.34E-06
vg1219585537 sf1219557007 12 19585537 1.73E-11 3.17E-10
vg1201520069 sf1201519069 12 1520069 3.54E-11 6.58E-07
vg1211781305 sf1211778641 12 11781305 4.64E-09 8.25E-09
vg0303857837 sf0303856833 3 3857837 7.78E-09 1.64E-06
vg1014485975 sf1014414741 10 14485975 8.90E-09 5.98E-09
vg0814220368 sf0814217654 8 14220368 NA 2.34E-07
vg0401412219 sf0401407769 4 1412219 NA 3.22E-07
vg0130961428 sf0130960384 1 30961428 NA 4.02E-07
vg0107013970 sf0107012970 1 7013970 NA 5.21E-07
vg1221698417 sf1221664964 12 21698417 NA 9.66E-07
vg0418704997 sf0418533044 4 18704997 NA 1.12E-06
vg0418844692 sf0418672737 4 18844692 NA 1.72E-06
vg1223507277 sf1223473737 12 23507277 NA 2.79E-06
vg1112018736 sf1112013053 11 12018736 NA 2.84E-06
vg1012521610 sf1012450425 10 12521610 NA 3.00E-06
vg0125147279 sf0125146235 1 25147279 NA 3.01E-06