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Detailed information for vg0208667468:
| Variant ID: vg0208667468 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 8667468 |
| 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: 127. )
Flanking Sequence (100 bp) in Reference Genome:
GCCTGATGAGCCTAAGCGTCAAGTGGTTCTCCCAGGCAAAAGAAAAATCGTCGGAGTTGAGGACAAGACTGACGAGGATTACGATCAGTTGGATGGGCAA[C/T]
CCCCTTTCACAGTGACGATTGACCCTAGCATCCTCCTATCAAATGAAGACACCCCTTACTCACGCAGCGATCACAAGGAGGGAACAATAGTGAGGAGAAA
Reverse complement sequence
TTTCTCCTCACTATTGTTCCCTCCTTGTGATCGCTGCGTGAGTAAGGGGTGTCTTCATTTGATAGGAGGATGCTAGGGTCAATCGTCACTGTGAAAGGGG[G/A]
TTGCCCATCCAACTGATCGTAATCCTCGTCAGTCTTGTCCTCAACTCCGACGATTTTTCTTTTGCCTGGGAGAACCACTTGACGCTTAGGCTCATCAGGC
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 | 5.80% | 0.40% | 8.53% | 85.25% | NA |
| All Indica | 2759 | 0.70% | 0.70% | 3.62% | 95.00% | NA |
| All Japonica | 1512 | 16.40% | 0.00% | 19.51% | 64.09% | NA |
| Aus | 269 | 0.00% | 0.00% | 1.49% | 98.51% | NA |
| Indica I | 595 | 0.50% | 0.20% | 4.87% | 94.45% | NA |
| Indica II | 465 | 0.60% | 0.20% | 0.65% | 98.49% | NA |
| Indica III | 913 | 0.00% | 0.90% | 1.75% | 97.37% | NA |
| Indica Intermediate | 786 | 1.80% | 1.00% | 6.62% | 90.59% | NA |
| Temperate Japonica | 767 | 18.00% | 0.00% | 32.20% | 49.80% | NA |
| Tropical Japonica | 504 | 19.40% | 0.00% | 4.76% | 75.79% | NA |
| Japonica Intermediate | 241 | 5.00% | 0.00% | 9.96% | 85.06% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Intermediate | 90 | 8.90% | 0.00% | 4.44% | 86.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0208667468 | C -> T | LOC_Os02g15470.1 | missense_variant ; p.Pro929Ser; MODERATE | nonsynonymous_codon ; P929S | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
0.627 |
DELETERIOUS | 0.01 |
| vg0208667468 | C -> DEL | LOC_Os02g15470.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |