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Detailed information for vg0815410455:
| Variant ID: vg0815410455 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 15410455 |
| 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: 227. )
Flanking Sequence (100 bp) in Reference Genome:
GTCTATCTTAGAGAACACAGTAGCTCCTTTCAGCTGATCGAACAGATCATCAATCCTTGGCAAAGGGTACTTGTTCTTAATAGTGACCTCATTGAGTGCG[C/T]
GGTAGTCCACGCACATCCTCTTGGTTTTGTCTTTCTTTTCCACAAAGATAACCGGAGCACCCCAAGGCGACGTGCTCGGGCGGATGTATCCCTTCTGTAA
Reverse complement sequence
TTACAGAAGGGATACATCCGCCCGAGCACGTCGCCTTGGGGTGCTCCGGTTATCTTTGTGGAAAAGAAAGACAAAACCAAGAGGATGTGCGTGGACTACC[G/A]
CGCACTCAATGAGGTCACTATTAAGAACAAGTACCCTTTGCCAAGGATTGATGATCTGTTCGATCAGCTGAAAGGAGCTACTGTGTTCTCTAAGATAGAC
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 | 20.20% | 0.10% | 11.24% | 68.41% | NA |
| All Indica | 2759 | 0.80% | 0.00% | 11.89% | 87.35% | NA |
| All Japonica | 1512 | 60.10% | 0.30% | 6.48% | 33.13% | NA |
| Aus | 269 | 0.70% | 0.00% | 34.57% | 64.68% | NA |
| Indica I | 595 | 0.20% | 0.00% | 0.50% | 99.33% | NA |
| Indica II | 465 | 1.30% | 0.00% | 8.17% | 90.54% | NA |
| Indica III | 913 | 0.20% | 0.00% | 20.37% | 79.41% | NA |
| Indica Intermediate | 786 | 1.50% | 0.00% | 12.85% | 85.62% | NA |
| Temperate Japonica | 767 | 83.80% | 0.00% | 2.09% | 14.08% | NA |
| Tropical Japonica | 504 | 27.40% | 1.00% | 10.12% | 61.51% | NA |
| Japonica Intermediate | 241 | 52.70% | 0.00% | 12.86% | 34.44% | NA |
| VI/Aromatic | 96 | 3.10% | 0.00% | 3.12% | 93.75% | NA |
| Intermediate | 90 | 25.60% | 0.00% | 10.00% | 64.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0815410455 | C -> T | LOC_Os08g25330.1 | missense_variant ; p.Arg644His; MODERATE | nonsynonymous_codon ; R644H | Average:5.196; most accessible tissue: Callus, score: 12.491 | benign  |
0.888 |
DELETERIOUS | 0.02 |
| vg0815410455 | C -> DEL | LOC_Os08g25330.1 | N | frameshift_variant | Average:5.196; most accessible tissue: Callus, score: 12.491 | N | N | N | N |