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Detailed information for vg1109585080:
| Variant ID: vg1109585080 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 9585080 |
| 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: 404. )
Flanking Sequence (100 bp) in Reference Genome:
AGGATTGTTGTTGTTCTTCTTCTGCTTCTTGAAGTTGGTGGTCTGCTGAGCTTTGTATTTCCCCTTGCTCTTGTTCTGGGCCTTGTGCACAACATTGGCA[C/T]
TGGACTGCCCACCATCGCCCTTAGACGCGACATCTTTTTCCCGAGCTTTCTCCTCAACATCAAGAGACGCTATCAACCCCTCAACGGAGTATTCCTGTCT
Reverse complement sequence
AGACAGGAATACTCCGTTGAGGGGTTGATAGCGTCTCTTGATGTTGAGGAGAAAGCTCGGGAAAAAGATGTCGCGTCTAAGGGCGATGGTGGGCAGTCCA[G/A]
TGCCAATGTTGTGCACAAGGCCCAGAACAAGAGCAAGGGGAAATACAAAGCTCAGCAGACCACCAACTTCAAGAAGCAGAAGAAGAACAACAACAATCCT
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 | 77.80% | 0.10% | 4.00% | 18.15% | NA |
| All Indica | 2759 | 94.90% | 0.00% | 3.62% | 1.45% | NA |
| All Japonica | 1512 | 45.50% | 0.00% | 1.59% | 52.91% | NA |
| Aus | 269 | 77.00% | 0.00% | 21.93% | 1.12% | NA |
| Indica I | 595 | 92.80% | 0.00% | 3.70% | 3.53% | NA |
| Indica II | 465 | 95.30% | 0.00% | 3.66% | 1.08% | NA |
| Indica III | 913 | 99.00% | 0.00% | 0.88% | 0.11% | NA |
| Indica Intermediate | 786 | 91.50% | 0.10% | 6.74% | 1.65% | NA |
| Temperate Japonica | 767 | 26.10% | 0.00% | 1.96% | 71.97% | NA |
| Tropical Japonica | 504 | 69.80% | 0.00% | 1.19% | 28.97% | NA |
| Japonica Intermediate | 241 | 56.40% | 0.00% | 1.24% | 42.32% | NA |
| VI/Aromatic | 96 | 89.60% | 1.00% | 3.12% | 6.25% | NA |
| Intermediate | 90 | 85.60% | 1.10% | 3.33% | 10.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1109585080 | C -> T | LOC_Os11g17200.1 | missense_variant ; p.Ser202Asn; MODERATE | nonsynonymous_codon ; S202N | Average:8.049; most accessible tissue: Zhenshan97 flag leaf, score: 16.47 | benign  |
0.34 |
DELETERIOUS | 0.02 |
| vg1109585080 | C -> DEL | LOC_Os11g17200.1 | N | frameshift_variant | Average:8.049; most accessible tissue: Zhenshan97 flag leaf, score: 16.47 | N | N | N | N |