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Detailed information for vg1117778472:
| Variant ID: vg1117778472 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 17778472 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 377. )
Flanking Sequence (100 bp) in Reference Genome:
GACGAGCTGACACTCGCCCTGCAGACTCCAGAGCATCCAGGACGAACACGAGGGAAAGGGGTGATTCCTTGGAAGATTGGTTTCAAGGAGGACATCCACA[C/T]
GTACAGGAGTCGGATGAGGAGCAAGAGAGATACCGAGGCGAAGATTGCAGACCTAGAGTTCCGGGTATCGAGCTACGAACTCAACATGCAAGAGGAGGTG
Reverse complement sequence
CACCTCCTCTTGCATGTTGAGTTCGTAGCTCGATACCCGGAACTCTAGGTCTGCAATCTTCGCCTCGGTATCTCTCTTGCTCCTCATCCGACTCCTGTAC[G/A]
TGTGGATGTCCTCCTTGAAACCAATCTTCCAAGGAATCACCCCTTTCCCTCGTGTTCGTCCTGGATGCTCTGGAGTCTGCAGGGCGAGTGTCAGCTCGTC
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 | 2.00% | 0.70% | 7.24% | 90.08% | NA |
| All Indica | 2759 | 3.20% | 0.70% | 9.89% | 86.23% | NA |
| All Japonica | 1512 | 0.20% | 0.70% | 1.72% | 97.35% | NA |
| Aus | 269 | 0.70% | 0.70% | 8.55% | 89.96% | NA |
| Indica I | 595 | 3.40% | 0.30% | 7.39% | 88.91% | NA |
| Indica II | 465 | 2.60% | 0.90% | 20.00% | 76.56% | NA |
| Indica III | 913 | 3.70% | 0.70% | 6.57% | 89.05% | NA |
| Indica Intermediate | 786 | 2.90% | 0.80% | 9.67% | 86.64% | NA |
| Temperate Japonica | 767 | 0.40% | 1.20% | 2.61% | 95.83% | NA |
| Tropical Japonica | 504 | 0.00% | 0.00% | 0.60% | 99.40% | NA |
| Japonica Intermediate | 241 | 0.00% | 0.80% | 1.24% | 97.93% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 11.46% | 88.54% | NA |
| Intermediate | 90 | 1.10% | 1.10% | 10.00% | 87.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1117778472 | C -> T | LOC_Os11g30552.1 | missense_variant ; p.Thr475Met; MODERATE | nonsynonymous_codon ; T475M | Average:5.208; most accessible tissue: Zhenshan97 root, score: 10.511 | probably damaging  |
2.771 |
DELETERIOUS | 0.02 |
| vg1117778472 | C -> DEL | LOC_Os11g30552.1 | N | frameshift_variant | Average:5.208; most accessible tissue: Zhenshan97 root, score: 10.511 | N | N | N | N |