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Detailed information for vg1112794841:
| Variant ID: vg1112794841 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 12794841 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 431. )
Flanking Sequence (100 bp) in Reference Genome:
CGACACTCAAGGCTGTTGTTGGCCCGATCTTTCGGTGAGTTGTGATAACTACGATTTGGGAGAAACGTTGACGATCCGACTACAACCGTACGAGACGTTG[T/C]
GTTGCGCCTTAGCGATCGATACACCTCTCCGTGGGTTGTTGATCTTGCCGGTGCAGATCAACCCTATTCCTGCAAGCAAATCGAAGAAACAAGCAAGAAC
Reverse complement sequence
GTTCTTGCTTGTTTCTTCGATTTGCTTGCAGGAATAGGGTTGATCTGCACCGGCAAGATCAACAACCCACGGAGAGGTGTATCGATCGCTAAGGCGCAAC[A/G]
CAACGTCTCGTACGGTTGTAGTCGGATCGTCAACGTTTCTCCCAAATCGTAGTTATCACAACTCACCGAAAGATCGGGCCAACAACAGCCTTGAGTGTCG
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 36.00% | 0.10% | 32.75% | 31.19% | NA |
| All Indica | 2759 | 41.10% | 0.10% | 30.77% | 27.98% | NA |
| All Japonica | 1512 | 24.80% | 0.00% | 36.84% | 38.36% | NA |
| Aus | 269 | 57.20% | 0.00% | 16.36% | 26.39% | NA |
| Indica I | 595 | 25.50% | 0.20% | 23.19% | 51.09% | NA |
| Indica II | 465 | 25.40% | 0.40% | 31.83% | 42.37% | NA |
| Indica III | 913 | 64.60% | 0.00% | 32.20% | 3.18% | NA |
| Indica Intermediate | 786 | 34.90% | 0.10% | 34.22% | 30.79% | NA |
| Temperate Japonica | 767 | 37.80% | 0.00% | 24.12% | 38.07% | NA |
| Tropical Japonica | 504 | 9.30% | 0.00% | 53.57% | 37.10% | NA |
| Japonica Intermediate | 241 | 15.80% | 0.00% | 42.32% | 41.91% | NA |
| VI/Aromatic | 96 | 10.40% | 0.00% | 70.83% | 18.75% | NA |
| Intermediate | 90 | 30.00% | 0.00% | 33.33% | 36.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1112794841 | T -> DEL | LOC_Os11g22320.1 | N | frameshift_variant | Average:9.316; most accessible tissue: Zhenshan97 flag leaf, score: 17.677 | N | N | N | N |
| vg1112794841 | T -> C | LOC_Os11g22320.1 | missense_variant ; p.His75Arg; MODERATE | nonsynonymous_codon ; H75R | Average:9.316; most accessible tissue: Zhenshan97 flag leaf, score: 17.677 | benign  |
0.185 |
TOLERATED | 0.10 |