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Detailed information for vg0135357983:
| Variant ID: vg0135357983 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 35357983 |
| 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: 359. )
Flanking Sequence (100 bp) in Reference Genome:
CGACCCTTTTTCACCCTTAACTTAGATGGATCTGGAATGTAAAAAACTTGGGCACTCAGCGTTGTGTAAGATCCTGAGATCCCGAACCCATATATCTCCT[C/T]
ACTCCATGTATGAAAGATTGCTTCTTTCCTGAAATAATTTGAGACGTACACATTGGGAGATATGCCACAATCACCGGCAGCAGCAAGAACGTGTGAGCAA
Reverse complement sequence
TTGCTCACACGTTCTTGCTGCTGCCGGTGATTGTGGCATATCTCCCAATGTGTACGTCTCAAATTATTTCAGGAAAGAAGCAATCTTTCATACATGGAGT[G/A]
AGGAGATATATGGGTTCGGGATCTCAGGATCTTACACAACGCTGAGTGCCCAAGTTTTTTACATTCCAGATCCATCTAAGTTAAGGGTGAAAAAGGGTCG
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 | 53.90% | 0.70% | 18.30% | 27.17% | NA |
| All Indica | 2759 | 44.10% | 1.10% | 27.15% | 27.69% | NA |
| All Japonica | 1512 | 65.80% | 0.00% | 3.11% | 31.08% | NA |
| Aus | 269 | 69.50% | 0.00% | 17.84% | 12.64% | NA |
| Indica I | 595 | 36.60% | 0.00% | 43.19% | 20.17% | NA |
| Indica II | 465 | 39.40% | 0.20% | 26.24% | 34.19% | NA |
| Indica III | 913 | 51.40% | 2.50% | 16.21% | 29.90% | NA |
| Indica Intermediate | 786 | 44.00% | 0.80% | 28.24% | 26.97% | NA |
| Temperate Japonica | 767 | 57.50% | 0.00% | 1.56% | 40.94% | NA |
| Tropical Japonica | 504 | 70.20% | 0.00% | 6.15% | 23.61% | NA |
| Japonica Intermediate | 241 | 83.00% | 0.00% | 1.66% | 15.35% | NA |
| VI/Aromatic | 96 | 94.80% | 0.00% | 3.12% | 2.08% | NA |
| Intermediate | 90 | 63.30% | 1.10% | 20.00% | 15.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0135357983 | C -> T | LOC_Os01g61090.1 | missense_variant ; p.Glu788Lys; MODERATE | nonsynonymous_codon ; E788K | Average:5.003; most accessible tissue: Zhenshan97 root, score: 10.511 | benign  |
0.917 |
DELETERIOUS | 0.04 |
| vg0135357983 | C -> DEL | LOC_Os01g61090.1 | N | frameshift_variant | Average:5.003; most accessible tissue: Zhenshan97 root, score: 10.511 | N | N | N | N |