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Detailed information for vg0719562525:
| Variant ID: vg0719562525 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 19562525 |
| 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: 272. )
Flanking Sequence (100 bp) in Reference Genome:
AAGTACGTATCTTAAGCACTGTAGGAAGGTTGTATACATGGGTCATCGTCGATTCCTTGCAGCAAACCACCCGGTACGGAAGAAAGGCAAGCACTTCGAA[C/T]
ATAAGGCCGACCACCGTACGAAGCCTAAATATCGCAGCGGGAAAACAGTGTTTGCTATGGTTAAAGATCTTAAAGTAGTGTTCGGAAAGGGGCCTGGAAG
Reverse complement sequence
CTTCCAGGCCCCTTTCCGAACACTACTTTAAGATCTTTAACCATAGCAAACACTGTTTTCCCGCTGCGATATTTAGGCTTCGTACGGTGGTCGGCCTTAT[G/A]
TTCGAAGTGCTTGCCTTTCTTCCGTACCGGGTGGTTTGCTGCAAGGAATCGACGATGACCCATGTATACAACCTTCCTACAGTGCTTAAGATACGTACTT
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 | 34.10% | 0.30% | 24.65% | 41.03% | NA |
| All Indica | 2759 | 35.70% | 0.10% | 17.40% | 46.72% | NA |
| All Japonica | 1512 | 36.40% | 0.00% | 33.53% | 30.03% | NA |
| Aus | 269 | 14.50% | 2.60% | 51.67% | 31.23% | NA |
| Indica I | 595 | 10.40% | 0.00% | 16.81% | 72.77% | NA |
| Indica II | 465 | 31.40% | 0.00% | 18.49% | 50.11% | NA |
| Indica III | 913 | 57.40% | 0.10% | 14.35% | 28.15% | NA |
| Indica Intermediate | 786 | 32.30% | 0.40% | 20.74% | 46.56% | NA |
| Temperate Japonica | 767 | 52.20% | 0.00% | 18.90% | 28.94% | NA |
| Tropical Japonica | 504 | 9.90% | 0.00% | 59.52% | 30.56% | NA |
| Japonica Intermediate | 241 | 41.90% | 0.00% | 25.73% | 32.37% | NA |
| VI/Aromatic | 96 | 5.20% | 0.00% | 16.67% | 78.12% | NA |
| Intermediate | 90 | 32.20% | 1.10% | 25.56% | 41.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0719562525 | C -> DEL | LOC_Os07g32740.1 | N | frameshift_variant | Average:6.027; most accessible tissue: Zhenshan97 root, score: 12.891 | N | N | N | N |
| vg0719562525 | C -> T | LOC_Os07g32740.1 | missense_variant ; p.His448Tyr; MODERATE | nonsynonymous_codon ; H448Y | Average:6.027; most accessible tissue: Zhenshan97 root, score: 12.891 | benign  |
0.769 |
DELETERIOUS | 0.00 |