Variant ID: vg0620536797 (JBrowse) | Variation Type: SNP |
Chromosome: chr06 | Position: 20536797 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GAGATTGCTGTTGACCAAAAATTTGCATGCCATGAGTTTCCTGAGAACACTAGAGTTAGAGCTGCTACTAGTGAGTTCATCGATTTTGCTTTGGTTTGGT[G/A]
GATAGAACATGGCAAGAAAAATCCTAATAACATGCCACAAACTTGGGATGCTTTGAAACGGGTCATGCGGGCTAGATTTGTTCCTTCTTACTATACACGT
ACGTGTATAGTAAGAAGGAACAAATCTAGCCCGCATGACCCGTTTCAAAGCATCCCAAGTTTGTGGCATGTTATTAGGATTTTTCTTGCCATGTTCTATC[C/T]
ACCAAACCAAAGCAAAATCGATGAACTCACTAGTAGCAGCTCTAACTCTAGTGTTCTCAGGAAACTCATGGCATGCAAATTTTTGGTCAACAGCAATCTC
Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 25.60% | 1.30% | 9.01% | 64.05% | NA |
All Indica | 2759 | 10.00% | 0.10% | 8.95% | 81.01% | NA |
All Japonica | 1512 | 42.00% | 3.80% | 6.15% | 48.02% | NA |
Aus | 269 | 88.50% | 0.00% | 6.32% | 5.20% | NA |
Indica I | 595 | 8.40% | 0.00% | 7.23% | 84.37% | NA |
Indica II | 465 | 9.20% | 0.00% | 7.53% | 83.23% | NA |
Indica III | 913 | 7.70% | 0.10% | 10.51% | 81.71% | NA |
Indica Intermediate | 786 | 14.20% | 0.10% | 9.29% | 76.34% | NA |
Temperate Japonica | 767 | 72.90% | 0.80% | 5.35% | 20.99% | NA |
Tropical Japonica | 504 | 6.30% | 1.60% | 3.37% | 88.69% | NA |
Japonica Intermediate | 241 | 18.30% | 18.30% | 14.52% | 48.96% | NA |
VI/Aromatic | 96 | 39.60% | 0.00% | 53.12% | 7.29% | NA |
Intermediate | 90 | 27.80% | 2.20% | 20.00% | 50.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0620536797 | G -> A | LOC_Os06g35210.1 | N | stop_gained | Average:13.233; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |
vg0620536797 | G -> DEL | LOC_Os06g35210.1 | N | frameshift_variant | Average:13.233; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0620536797 | NA | 4.97E-07 | mr1403 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
vg0620536797 | 1.91E-06 | 1.91E-06 | mr1520 | Jap_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
vg0620536797 | NA | 8.95E-06 | mr1729 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
vg0620536797 | NA | 3.56E-06 | mr1082_2 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
vg0620536797 | NA | 4.80E-06 | mr1083_2 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
vg0620536797 | 4.92E-08 | 1.11E-12 | mr1408_2 | All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
vg0620536797 | NA | 6.37E-08 | mr1408_2 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |