Search for Variation information by Variation ID:
Detailed information for vg0817015878:
| Variant ID: vg0817015878 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17015878 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GTTGTACCTTTGGAAGTTCCAATACAGCAGCTGAGAAATCAAGTACAAGATGAAGAACCCGAGTGTAAGAAAGTTATTGTTTGTTACAACTGCAATGAAG[A/C]
AGGGCATTACTCCAAAAACTGTCCCCAACCAAGGCAAAATCGACCTCCACATTACCGCCAATTTACACGAAGCAGACATTCCAATCGTATTGTGGTCACT
Reverse complement sequence
AGTGACCACAATACGATTGGAATGTCTGCTTCGTGTAAATTGGCGGTAATGTGGAGGTCGATTTTGCCTTGGTTGGGGACAGTTTTTGGAGTAATGCCCT[T/G]
CTTCATTGCAGTTGTAACAAACAATAACTTTCTTACACTCGGGTTCTTCATCTTGTACTTGATTTCTCAGCTGCTGTATTGGAACTTCCAAAGGTACAAC
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 30.50% | 0.10% | 19.00% | 50.40% | NA |
| All Indica | 2759 | 13.00% | 0.10% | 25.05% | 61.80% | NA |
| All Japonica | 1512 | 62.90% | 0.10% | 3.97% | 33.07% | NA |
| Aus | 269 | 20.10% | 0.00% | 36.43% | 43.49% | NA |
| Indica I | 595 | 7.10% | 0.00% | 9.41% | 83.53% | NA |
| Indica II | 465 | 3.00% | 0.00% | 25.38% | 71.61% | NA |
| Indica III | 913 | 23.30% | 0.30% | 34.83% | 41.51% | NA |
| Indica Intermediate | 786 | 11.60% | 0.00% | 25.32% | 63.10% | NA |
| Temperate Japonica | 767 | 79.80% | 0.00% | 1.04% | 19.17% | NA |
| Tropical Japonica | 504 | 35.90% | 0.20% | 8.93% | 54.96% | NA |
| Japonica Intermediate | 241 | 65.60% | 0.00% | 2.90% | 31.54% | NA |
| VI/Aromatic | 96 | 39.60% | 0.00% | 39.58% | 20.83% | NA |
| Intermediate | 90 | 42.20% | 1.10% | 12.22% | 44.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0817015878 | A -> C | LOC_Os08g27910.1 | missense_variant ; p.Glu429Ala; MODERATE | nonsynonymous_codon ; E429S | Average:5.698; most accessible tissue: Callus, score: 10.152 | benign  |
1.299 |
DELETERIOUS | 0.02 |
| vg0817015878 | A -> DEL | LOC_Os08g27910.1 | N | frameshift_variant | Average:5.698; most accessible tissue: Callus, score: 10.152 | N | N | N | N |