Search for Variation information by Variation ID:
Detailed information for vg1112794815:
| Variant ID: vg1112794815 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 12794815 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 431. )
Flanking Sequence (100 bp) in Reference Genome:
CCACCTGATGAACCCTGAGTTCCTCTCGACACTCAAGGCTGTTGTTGGCCCGATCTTTCGGTGAGTTGTGATAACTACGATTTGGGAGAAACGTTGACGA[T/A]
CCGACTACAACCGTACGAGACGTTGTGTTGCGCCTTAGCGATCGATACACCTCTCCGTGGGTTGTTGATCTTGCCGGTGCAGATCAACCCTATTCCTGCA
Reverse complement sequence
TGCAGGAATAGGGTTGATCTGCACCGGCAAGATCAACAACCCACGGAGAGGTGTATCGATCGCTAAGGCGCAACACAACGTCTCGTACGGTTGTAGTCGG[A/T]
TCGTCAACGTTTCTCCCAAATCGTAGTTATCACAACTCACCGAAAGATCGGGCCAACAACAGCCTTGAGTGTCGAGAGGAACTCAGGGTTCATCAGGTGG
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 32.90% | 0.10% | 35.38% | 31.55% | NA |
| All Indica | 2759 | 36.10% | 0.20% | 35.01% | 28.67% | NA |
| All Japonica | 1512 | 24.80% | 0.00% | 37.04% | 38.16% | NA |
| Aus | 269 | 57.20% | 0.00% | 16.36% | 26.39% | NA |
| Indica I | 595 | 21.80% | 0.20% | 25.55% | 52.44% | NA |
| Indica II | 465 | 23.40% | 0.60% | 33.12% | 42.80% | NA |
| Indica III | 913 | 55.20% | 0.10% | 41.18% | 3.50% | NA |
| Indica Intermediate | 786 | 32.20% | 0.10% | 36.13% | 31.55% | NA |
| Temperate Japonica | 767 | 37.80% | 0.00% | 24.64% | 37.55% | NA |
| Tropical Japonica | 504 | 9.30% | 0.00% | 53.57% | 37.10% | NA |
| Japonica Intermediate | 241 | 15.80% | 0.00% | 41.91% | 42.32% | NA |
| VI/Aromatic | 96 | 10.40% | 0.00% | 70.83% | 18.75% | NA |
| Intermediate | 90 | 24.40% | 0.00% | 37.78% | 37.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1112794815 | T -> A | LOC_Os11g22320.1 | missense_variant ; p.Ile84Phe; MODERATE | nonsynonymous_codon ; I84F | Average:9.159; most accessible tissue: Zhenshan97 flag leaf, score: 14.027 | possibly damaging  |
1.85 |
DELETERIOUS | 0.00 |
| vg1112794815 | T -> DEL | LOC_Os11g22320.1 | N | frameshift_variant | Average:9.159; most accessible tissue: Zhenshan97 flag leaf, score: 14.027 | N | N | N | N |