Search for Variation information by Variation ID:
Detailed information for vg0118270700:
| Variant ID: vg0118270700 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 18270700 |
| Reference Allele: G | Alternative Allele: A,GAACACCAATGGAGGTTGCGGTGCGGAAGATTGCTATGTACTGGTTCAAGAACCAGATTGCTACGTACTGGTTCGAGAACCAGCGAGCTAGTAGAATCATCTCTCA |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 286. )
Flanking Sequence (100 bp) in Reference Genome:
CCAATGGAGGTTGCGGTGCGGGAGATTGCTACGTACTGGTTCAAGAACCAGATTGCTACGTACTGGTTCGAGAACCAGCGAGCGAGTAGAATCATCTCTC[G/A,GAACACCAATGGAGGTTGCGGTGCGGAAGATTGCTATGTACTGGTTCAAGAACCAGATTGCTACGTACTGGTTCGAGAACCAGCGAGCTAGTAGAATCATCTCTCA]
AACACCAATGGAGGTTGTGGTGTAGGAGATTGCTACGTACTGGTTCGAGAACCAGCGAGCGAGTAGAATCATCTCTCGAACACGAATGAAAGTGCTAGAG
Reverse complement sequence
CTCTAGCACTTTCATTCGTGTTCGAGAGATGATTCTACTCGCTCGCTGGTTCTCGAACCAGTACGTAGCAATCTCCTACACCACAACCTCCATTGGTGTT[C/T,TGAGAGATGATTCTACTAGCTCGCTGGTTCTCGAACCAGTACGTAGCAATCTGGTTCTTGAACCAGTACATAGCAATCTTCCGCACCGCAACCTCCATTGGTGTTC]
GAGAGATGATTCTACTCGCTCGCTGGTTCTCGAACCAGTACGTAGCAATCTGGTTCTTGAACCAGTACGTAGCAATCTCCCGCACCGCAACCTCCATTGG
Allele Frequencies:
| 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 | 79.00% | 0.50% | 11.98% | 8.51% | NA |
| All Indica | 2759 | 68.50% | 0.60% | 18.99% | 11.92% | NA |
| All Japonica | 1512 | 99.10% | 0.10% | 0.66% | 0.13% | NA |
| Aus | 269 | 64.70% | 1.50% | 8.92% | 24.91% | NA |
| Indica I | 595 | 38.50% | 0.00% | 41.85% | 19.66% | NA |
| Indica II | 465 | 78.90% | 0.20% | 16.13% | 4.73% | NA |
| Indica III | 913 | 80.30% | 1.10% | 6.90% | 11.72% | NA |
| Indica Intermediate | 786 | 71.20% | 0.80% | 17.43% | 10.56% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 97.80% | 0.40% | 1.59% | 0.20% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.00% | 0.83% | 0.41% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 1.04% | 1.04% | NA |
| Intermediate | 90 | 88.90% | 0.00% | 7.78% | 3.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0118270700 | G -> GAACACCAATGGAGGTTGCGGTGCGGAAGA TTGCTATGTACTGGTTCAAGAACCAGATTG CTACGTACTGGTTCGAGAACCAGCGAGCTA GTAGAATCATCTCTCA | LOC_Os01g33180.1 | disruptive_inframe_insertion ; p.Val90_Val91insAlaValArgLysIl eAlaMetTyrTrpPheLysAsnGlnIleAl aThrTyrTrpPheGluAsnGlnArgAlaSe rArgIleIleSerGlnThrProMetGluVa l; MODERATE | N | Average:54.279; most accessible tissue: Minghui63 young leaf, score: 70.655 | N | N | N | N |
| vg0118270700 | G -> GAACACCAATGGAGGTTGCGGTGCGGAAGA TTGCTATGTACTGGTTCAAGAACCAGATTG CTACGTACTGGTTCGAGAACCAGCGAGCTA GTAGAATCATCTCTCA | LOC_Os01g33160.1 | downstream_gene_variant ; 3503.0bp to feature; MODIFIER | N | Average:54.279; most accessible tissue: Minghui63 young leaf, score: 70.655 | N | N | N | N |
| vg0118270700 | G -> GAACACCAATGGAGGTTGCGGTGCGGAAGA TTGCTATGTACTGGTTCAAGAACCAGATTG CTACGTACTGGTTCGAGAACCAGCGAGCTA GTAGAATCATCTCTCA | LOC_Os01g33190.1 | downstream_gene_variant ; 1782.0bp to feature; MODIFIER | N | Average:54.279; most accessible tissue: Minghui63 young leaf, score: 70.655 | N | N | N | N |
| vg0118270700 | G -> A | LOC_Os01g33180.1 | missense_variant ; p.Arg85Gln; MODERATE | nonsynonymous_codon ; R85Q | Average:54.279; most accessible tissue: Minghui63 young leaf, score: 70.655 | benign  |
0.582 |
DELETERIOUS | 0.00 |
| vg0118270700 | G -> DEL | LOC_Os01g33180.1 | N | frameshift_variant | Average:54.279; most accessible tissue: Minghui63 young leaf, score: 70.655 | N | N | N | N |