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Detailed information for vg1114173044:
| Variant ID: vg1114173044 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 14173044 |
| 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: 350. )
Flanking Sequence (100 bp) in Reference Genome:
GCCTGGAAGCCAGCATATAGAGAGCGAAGATGGTCACGCGGCGATGTGGAAAAAGAACTCTATATTTTGGGAGTTACCATATTGGGAATTCTTGGACGTA[C/T]
GCCACGCAATCGACGTGATGCACCTCACTAAGAACCTTTGCGTAAACCTTCTTGGCTTCCTAGGTGTATACGGAAAGTCGAAAGATACACTGGAAGCACG
Reverse complement sequence
CGTGCTTCCAGTGTATCTTTCGACTTTCCGTATACACCTAGGAAGCCAAGAAGGTTTACGCAAAGGTTCTTAGTGAGGTGCATCACGTCGATTGCGTGGC[G/A]
TACGTCCAAGAATTCCCAATATGGTAACTCCCAAAATATAGAGTTCTTTTTCCACATCGCCGCGTGACCATCTTCGCTCTCTATATGCTGGCTTCCAGGC
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 | 3.00% | 0.70% | 11.57% | 84.74% | NA |
| All Indica | 2759 | 4.50% | 1.10% | 11.63% | 82.71% | NA |
| All Japonica | 1512 | 0.50% | 0.10% | 12.17% | 87.17% | NA |
| Aus | 269 | 1.90% | 0.40% | 5.95% | 91.82% | NA |
| Indica I | 595 | 3.90% | 0.20% | 11.43% | 84.54% | NA |
| Indica II | 465 | 6.90% | 0.90% | 8.39% | 83.87% | NA |
| Indica III | 913 | 3.90% | 1.80% | 13.91% | 80.39% | NA |
| Indica Intermediate | 786 | 4.30% | 1.30% | 11.07% | 83.33% | NA |
| Temperate Japonica | 767 | 0.50% | 0.00% | 8.74% | 90.74% | NA |
| Tropical Japonica | 504 | 0.60% | 0.40% | 17.86% | 81.15% | NA |
| Japonica Intermediate | 241 | 0.40% | 0.00% | 11.20% | 88.38% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 19.79% | 80.21% | NA |
| Intermediate | 90 | 2.20% | 0.00% | 7.78% | 90.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1114173044 | C -> T | LOC_Os11g24860.1 | missense_variant ; p.Arg559Cys; MODERATE | nonsynonymous_codon ; R559C | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
1.11 |
DELETERIOUS | 0.02 |
| vg1114173044 | C -> DEL | LOC_Os11g24860.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |