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Detailed information for vg0118270591:
| Variant ID: vg0118270591 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 18270591 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 327. )
Flanking Sequence (100 bp) in Reference Genome:
CCAGCGAGCGAGTAGAATCATCTCTCAAACACCAATGGAGGTTGCGGTGCGGGAGATTGCTACGTACTGGTTCGAGAACCAGCGAGCAAGTAGAATCATC[T/C]
CTCGAACACCAATGGAGGTTGCGGTGCGGGAGATTGCTACGTACTGGTTCAAGAACCAGATTGCTACGTACTGGTTCGAGAACCAGCGAGCGAGTAGAAT
Reverse complement sequence
ATTCTACTCGCTCGCTGGTTCTCGAACCAGTACGTAGCAATCTGGTTCTTGAACCAGTACGTAGCAATCTCCCGCACCGCAACCTCCATTGGTGTTCGAG[A/G]
GATGATTCTACTTGCTCGCTGGTTCTCGAACCAGTACGTAGCAATCTCCCGCACCGCAACCTCCATTGGTGTTTGAGAGATGATTCTACTCGCTCGCTGG
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.30% | 0.70% | 1.50% | 0.53% | NA |
| All Indica | 2759 | 95.50% | 1.10% | 2.54% | 0.91% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.20% | 0.00% | 1.68% | 0.17% | NA |
| Indica II | 465 | 94.40% | 1.10% | 3.66% | 0.86% | NA |
| Indica III | 913 | 93.60% | 1.80% | 2.74% | 1.86% | NA |
| Indica Intermediate | 786 | 96.20% | 1.10% | 2.29% | 0.38% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 1.10% | 1.11% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0118270591 | T -> DEL | LOC_Os01g33180.1 | N | frameshift_variant | Average:53.336; most accessible tissue: Minghui63 young leaf, score: 74.514 | N | N | N | N |
| vg0118270591 | T -> C | LOC_Os01g33180.1 | missense_variant ; p.Ser49Pro; MODERATE | nonsynonymous_codon ; S49P | Average:53.336; most accessible tissue: Minghui63 young leaf, score: 74.514 | probably damaging  |
2.042 |
DELETERIOUS | 0.00 |