Search for Variation information by Variation ID:
Detailed information for vg0108457613:
| Variant ID: vg0108457613 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 8457613 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GATATCGACTTGAAGGATAGGCATGGCTATTCCCCTACGGTGTCTCCGGATACCGTCAGGAGATACGAAAGCGCTATCTCTGATCTCGCCGGGCACAGAT[T/C]
CGAGGAGGAAGACTACCCTGTTGTCGACTACGAGTCAGACCTTCAGACCGACATGTCCACAACAGTTAGATAGGCTACCCACATATTGTACTGGTGTGAT
Reverse complement sequence
ATCACACCAGTACAATATGTGGGTAGCCTATCTAACTGTTGTGGACATGTCGGTCTGAAGGTCTGACTCGTAGTCGACAACAGGGTAGTCTTCCTCCTCG[A/G]
ATCTGTGCCCGGCGAGATCAGAGATAGCGCTTTCGTATCTCCTGACGGTATCCGGAGACACCGTAGGGGAATAGCCATGCCTATCCTTCAAGTCGATATC
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 | 75.70% | 0.00% | 5.40% | 18.92% | NA |
| All Indica | 2759 | 68.10% | 0.00% | 6.63% | 25.26% | NA |
| All Japonica | 1512 | 87.60% | 0.00% | 3.04% | 9.39% | NA |
| Aus | 269 | 76.60% | 0.40% | 7.06% | 15.99% | NA |
| Indica I | 595 | 77.50% | 0.00% | 4.37% | 18.15% | NA |
| Indica II | 465 | 68.60% | 0.00% | 5.16% | 26.24% | NA |
| Indica III | 913 | 59.40% | 0.00% | 8.87% | 31.76% | NA |
| Indica Intermediate | 786 | 70.90% | 0.00% | 6.62% | 22.52% | NA |
| Temperate Japonica | 767 | 97.70% | 0.00% | 0.52% | 1.83% | NA |
| Tropical Japonica | 504 | 71.20% | 0.00% | 6.75% | 22.02% | NA |
| Japonica Intermediate | 241 | 89.60% | 0.00% | 3.32% | 7.05% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 2.08% | 2.08% | NA |
| Intermediate | 90 | 83.30% | 0.00% | 5.56% | 11.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0108457613 | T -> DEL | LOC_Os01g15070.1 | N | frameshift_variant | Average:53.082; most accessible tissue: Zhenshan97 panicle, score: 67.02 | N | N | N | N |
| vg0108457613 | T -> C | LOC_Os01g15070.1 | missense_variant ; p.Phe63Ser; MODERATE | nonsynonymous_codon ; F63S | Average:53.082; most accessible tissue: Zhenshan97 panicle, score: 67.02 | benign  |
0.712 |
DELETERIOUS | 0.03 |