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Detailed information for vg1120596236:
| Variant ID: vg1120596236 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 20596236 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AAACCAACCTGGAATCGACATAGATGTTTTCCTTGAGCCTTTGATGGAGGACATGGAGGAGCTTTGGAAAGAGGGGTTACAACTATGGGATGAGTTTAAG[C/T]
GGGAGCACTTCAATCTACGTGCGATCATATTCGTTACCATCAATGACCTACCTGCAAACTTTTCATTATCTGGGCAGATTAAAGGGAAGACTGGATGTCT
Reverse complement sequence
AGACATCCAGTCTTCCCTTTAATCTGCCCAGATAATGAAAAGTTTGCAGGTAGGTCATTGATGGTAACGAATATGATCGCACGTAGATTGAAGTGCTCCC[G/A]
CTTAAACTCATCCCATAGTTGTAACCCCTCTTTCCAAAGCTCCTCCATGTCCTCCATCAAAGGCTCAAGGAAAACATCTATGTCGATTCCAGGTTGGTTT
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 | 29.80% | 0.20% | 5.40% | 64.66% | NA |
| All Indica | 2759 | 13.20% | 0.00% | 4.89% | 81.95% | NA |
| All Japonica | 1512 | 59.60% | 0.60% | 6.48% | 33.33% | NA |
| Aus | 269 | 6.30% | 0.00% | 5.58% | 88.10% | NA |
| Indica I | 595 | 48.20% | 0.00% | 3.19% | 48.57% | NA |
| Indica II | 465 | 1.70% | 0.00% | 4.30% | 93.98% | NA |
| Indica III | 913 | 2.20% | 0.00% | 5.91% | 91.89% | NA |
| Indica Intermediate | 786 | 6.10% | 0.00% | 5.34% | 88.55% | NA |
| Temperate Japonica | 767 | 75.10% | 0.00% | 7.17% | 17.73% | NA |
| Tropical Japonica | 504 | 47.20% | 1.80% | 5.16% | 45.83% | NA |
| Japonica Intermediate | 241 | 36.10% | 0.00% | 7.05% | 56.85% | NA |
| VI/Aromatic | 96 | 89.60% | 0.00% | 1.04% | 9.38% | NA |
| Intermediate | 90 | 43.30% | 0.00% | 6.67% | 50.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1120596236 | C -> T | LOC_Os11g35130.1 | missense_variant ; p.Arg303Trp; MODERATE | nonsynonymous_codon ; R303W | Average:5.97; most accessible tissue: Zhenshan97 flower, score: 13.891 | benign  |
0.93 |
DELETERIOUS | 0.02 |
| vg1120596236 | C -> DEL | LOC_Os11g35130.1 | N | frameshift_variant | Average:5.97; most accessible tissue: Zhenshan97 flower, score: 13.891 | N | N | N | N |