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Detailed information for vg0118270613:
| Variant ID: vg0118270613 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 18270613 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 327. )
Flanking Sequence (100 bp) in Reference Genome:
TCTCAAACACCAATGGAGGTTGCGGTGCGGGAGATTGCTACGTACTGGTTCGAGAACCAGCGAGCAAGTAGAATCATCTCTCGAACACCAATGGAGGTTG[C/T]
GGTGCGGGAGATTGCTACGTACTGGTTCAAGAACCAGATTGCTACGTACTGGTTCGAGAACCAGCGAGCGAGTAGAATCATCTCTCGAACACCAATGGAG
Reverse complement sequence
CTCCATTGGTGTTCGAGAGATGATTCTACTCGCTCGCTGGTTCTCGAACCAGTACGTAGCAATCTGGTTCTTGAACCAGTACGTAGCAATCTCCCGCACC[G/A]
CAACCTCCATTGGTGTTCGAGAGATGATTCTACTTGCTCGCTGGTTCTCGAACCAGTACGTAGCAATCTCCCGCACCGCAACCTCCATTGGTGTTTGAGA
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 | 98.90% | 0.00% | 1.08% | 0.00% | NA |
| All Indica | 2759 | 98.10% | 0.00% | 1.85% | 0.00% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 91.00% | 0.20% | 8.82% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.70% | 0.00% | 1.27% | 0.00% | 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 | 100.00% | 0.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0118270613 | C -> T | LOC_Os01g33180.1 | missense_variant ; p.Ala56Val; MODERATE | nonsynonymous_codon ; A56V | Average:52.105; most accessible tissue: Minghui63 young leaf, score: 71.254 | benign  |
0.572 |
TOLERATED | 0.15 |