Search for Variation information by Variation ID:
Detailed information for vg0118270631:
| Variant ID: vg0118270631 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 18270631 |
| Reference Allele: C | Alternative Allele: T,CGTACTGGTTCAAGAACCAGATTGCTACGTACTGGTTCGAGAACCAGCGAGCGAGTAGAATCATCTCTCGAACACCAATGGAGGTTGCGGTGCGGAAGATTGCTAT |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.89, T: 0.11, others allele: 0.00, population size: 272. )
Flanking Sequence (100 bp) in Reference Genome:
GTTGCGGTGCGGGAGATTGCTACGTACTGGTTCGAGAACCAGCGAGCAAGTAGAATCATCTCTCGAACACCAATGGAGGTTGCGGTGCGGGAGATTGCTA[C/T,CGTACTGGTTCAAGAACCAGATTGCTACGTACTGGTTCGAGAACCAGCGAGCGAGTAGAATCATCTCTCGAACACCAATGGAGGTTGCGGTGCGGAAGATTGCTAT]
GTACTGGTTCAAGAACCAGATTGCTACGTACTGGTTCGAGAACCAGCGAGCGAGTAGAATCATCTCTCGAACACCAATGGAGGTTGTGGTGTAGGAGATT
Reverse complement sequence
AATCTCCTACACCACAACCTCCATTGGTGTTCGAGAGATGATTCTACTCGCTCGCTGGTTCTCGAACCAGTACGTAGCAATCTGGTTCTTGAACCAGTAC[G/A,ATAGCAATCTTCCGCACCGCAACCTCCATTGGTGTTCGAGAGATGATTCTACTCGCTCGCTGGTTCTCGAACCAGTACGTAGCAATCTGGTTCTTGAACCAGTACG]
TAGCAATCTCCCGCACCGCAACCTCCATTGGTGTTCGAGAGATGATTCTACTTGCTCGCTGGTTCTCGAACCAGTACGTAGCAATCTCCCGCACCGCAAC
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 63.50% | 0.80% | 7.41% | 27.93% | CGTACTGGTTCAAGAACCAGATTGCTACGTACTGGTTCGAGAACCAGCGAGCGAGTAGAATCATCTCTCGAACACCAATGGAGGTTGCGGTGCGGAAGATTGCTAT: 0.38% |
| All Indica | 2759 | 45.80% | 1.20% | 11.27% | 41.25% | CGTACTGGTTCAAGAACCAGATTGCTACGTACTGGTTCGAGAACCAGCGAGCGAGTAGAATCATCTCTCGAACACCAATGGAGGTTGCGGTGCGGAAGATTGCTAT: 0.54% |
| All Japonica | 1512 | 97.90% | 0.10% | 0.60% | 1.32% | NA |
| Aus | 269 | 36.10% | 1.90% | 7.81% | 53.53% | CGTACTGGTTCAAGAACCAGATTGCTACGTACTGGTTCGAGAACCAGCGAGCGAGTAGAATCATCTCTCGAACACCAATGGAGGTTGCGGTGCGGAAGATTGCTAT: 0.74% |
| Indica I | 595 | 12.90% | 0.50% | 15.97% | 69.75% | CGTACTGGTTCAAGAACCAGATTGCTACGTACTGGTTCGAGAACCAGCGAGCGAGTAGAATCATCTCTCGAACACCAATGGAGGTTGCGGTGCGGAAGATTGCTAT: 0.84% |
| Indica II | 465 | 65.40% | 0.40% | 9.25% | 24.95% | NA |
| Indica III | 913 | 54.70% | 2.30% | 9.75% | 32.53% | CGTACTGGTTCAAGAACCAGATTGCTACGTACTGGTTCGAGAACCAGCGAGCGAGTAGAATCATCTCTCGAACACCAATGGAGGTTGCGGTGCGGAAGATTGCTAT: 0.77% |
| Indica Intermediate | 786 | 48.70% | 0.80% | 10.69% | 39.44% | CGTACTGGTTCAAGAACCAGATTGCTACGTACTGGTTCGAGAACCAGCGAGCGAGTAGAATCATCTCTCGAACACCAATGGAGGTTGCGGTGCGGAAGATTGCTAT: 0.38% |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 95.00% | 0.20% | 1.59% | 3.17% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.40% | 0.00% | 1.66% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 1.04% | 3.12% | NA |
| Intermediate | 90 | 73.30% | 0.00% | 8.89% | 16.67% | CGTACTGGTTCAAGAACCAGATTGCTACGTACTGGTTCGAGAACCAGCGAGCGAGTAGAATCATCTCTCGAACACCAATGGAGGTTGCGGTGCGGAAGATTGCTAT: 1.11% |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0118270631 | C -> T | LOC_Os01g33180.1 | missense_variant ; p.Thr62Met; MODERATE | nonsynonymous_codon ; T62M | Average:51.295; most accessible tissue: Minghui63 young leaf, score: 70.038 | benign  |
0.786 |
DELETERIOUS | 0.00 |
| vg0118270631 | C -> CGTACTGGTTCAAGAACCAGATTGCTACGT ACTGGTTCGAGAACCAGCGAGCGAGTAGAA TCATCTCTCGAACACCAATGGAGGTTGCGG TGCGGAAGATTGCTAT | LOC_Os01g33180.1 | disruptive_inframe_insertion ; p.Val90_Val91insAlaValArgLysIl eAlaMetTyrTrpPheLysAsnGlnIleAl aThrTyrTrpPheGluAsnGlnArgAlaSe rArgIleIleSerArgThrProMetGluVa l; MODERATE | inframe_variant | Average:51.295; most accessible tissue: Minghui63 young leaf, score: 70.038 | N | N | N | N |
| vg0118270631 | C -> DEL | LOC_Os01g33180.1 | N | frameshift_variant | Average:51.295; most accessible tissue: Minghui63 young leaf, score: 70.038 | N | N | N | N |