Search for Variation information by Variation ID:
Detailed information for vg0719562406:
| Variant ID: vg0719562406 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 19562406 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 291. )
Flanking Sequence (100 bp) in Reference Genome:
GAGTTTAACCTACGAGCGCTGCTGTTCGTAACCATCAACGATTGGCCTGTACTTAGCAACCTATCCGGACAGTCCAACAAGGGGTACAAGGCTTGCACTC[A/G]
CTGTATGGATGAAACAGAAAGTACGTATCTTAAGCACTGTAGGAAGGTTGTATACATGGGTCATCGTCGATTCCTTGCAGCAAACCACCCGGTACGGAAG
Reverse complement sequence
CTTCCGTACCGGGTGGTTTGCTGCAAGGAATCGACGATGACCCATGTATACAACCTTCCTACAGTGCTTAAGATACGTACTTTCTGTTTCATCCATACAG[T/C]
GAGTGCAAGCCTTGTACCCCTTGTTGGACTGTCCGGATAGGTTGCTAAGTACAGGCCAATCGTTGATGGTTACGAACAGCAGCGCTCGTAGGTTAAACTC
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 2.20% | 0.30% | 41.52% | 55.95% | NA |
| All Indica | 2759 | 0.90% | 0.10% | 24.28% | 74.74% | NA |
| All Japonica | 1512 | 5.00% | 0.70% | 71.49% | 22.75% | NA |
| Aus | 269 | 0.70% | 0.00% | 65.43% | 33.83% | NA |
| Indica I | 595 | 0.50% | 0.00% | 4.37% | 95.13% | NA |
| Indica II | 465 | 0.20% | 0.40% | 22.15% | 77.20% | NA |
| Indica III | 913 | 0.80% | 0.10% | 40.96% | 58.16% | NA |
| Indica Intermediate | 786 | 1.70% | 0.00% | 21.25% | 77.10% | NA |
| Temperate Japonica | 767 | 5.20% | 0.10% | 76.40% | 18.25% | NA |
| Tropical Japonica | 504 | 4.80% | 1.60% | 63.89% | 29.76% | NA |
| Japonica Intermediate | 241 | 5.00% | 0.80% | 71.78% | 22.41% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 3.12% | 96.88% | NA |
| Intermediate | 90 | 3.30% | 1.10% | 35.56% | 60.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0719562406 | A -> DEL | LOC_Os07g32740.1 | N | frameshift_variant | Average:6.027; most accessible tissue: Zhenshan97 root, score: 12.891 | N | N | N | N |
| vg0719562406 | A -> G | LOC_Os07g32740.1 | missense_variant ; p.His408Arg; MODERATE | nonsynonymous_codon ; H408R | Average:6.027; most accessible tissue: Zhenshan97 root, score: 12.891 | benign  |
0.844 |
DELETERIOUS | 0.00 |