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Detailed information for vg0135985103:
| Variant ID: vg0135985103 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 35985103 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 331. )
Flanking Sequence (100 bp) in Reference Genome:
CAGACATTGCTGTTAGGCTGAGCTGAAGAGCACATGAGGATGTGCGTTGTGTCTATGGCGCCGCAGCAGTTGGGGAGGCCCTGAATCTTTTCAAACTTAG[A/C]
TTTGACGGTTGCCATCTCCTCAGGAGTAGGCCACTTAAGATGATTGGCAGCGCGCTCCTCCAAGGCCTCAATAAACTTCCAAGTGATGTTTGAGATAGCT
Reverse complement sequence
AGCTATCTCAAACATCACTTGGAAGTTTATTGAGGCCTTGGAGGAGCGCGCTGCCAATCATCTTAAGTGGCCTACTCCTGAGGAGATGGCAACCGTCAAA[T/G]
CTAAGTTTGAAAAGATTCAGGGCCTCCCCAACTGCTGCGGCGCCATAGACACAACGCACATCCTCATGTGCTCTTCAGCTCAGCCTAACAGCAATGTCTG
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 66.50% | 33.20% | 0.15% | 0.08% | NA |
| All Indica | 2759 | 98.50% | 1.20% | 0.18% | 0.14% | NA |
| All Japonica | 1512 | 2.10% | 97.90% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.70% | 0.00% | 0.17% | 0.17% | NA |
| Indica II | 465 | 99.40% | 0.40% | 0.22% | 0.00% | NA |
| Indica III | 913 | 99.50% | 0.40% | 0.00% | 0.11% | NA |
| Indica Intermediate | 786 | 96.10% | 3.30% | 0.38% | 0.25% | NA |
| Temperate Japonica | 767 | 1.20% | 98.80% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 2.80% | 97.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 3.30% | 96.70% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 83.30% | 16.70% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 51.10% | 46.70% | 2.22% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0135985103 | A -> DEL | LOC_Os01g62160.1 | N | frameshift_variant | Average:74.512; most accessible tissue: Zhenshan97 flower, score: 86.194 | N | N | N | N |
| vg0135985103 | A -> C | LOC_Os01g62160.1 | missense_variant ; p.Ser159Ala; MODERATE | nonsynonymous_codon ; S159A | Average:74.512; most accessible tissue: Zhenshan97 flower, score: 86.194 | benign  |
0.336 |
TOLERATED | 0.28 |