Search for Variation information by Variation ID:
Detailed information for vg1218480608:
| Variant ID: vg1218480608 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18480608 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ATCCTCTTGGTGTATCTACAAGTGGCAACGTGGTGCAATGCCGTCTCAGTCTCGCGGCGGCAAAGAGGGCAACAACCATTGTTCTGCCATCCCCTGGTCG[C/T]
AAGCCGGTCTAAAGTCCAGACTCTGTTCTGAATGATGAGCCAAGCATGAAATTTGCATTTCCCCGGCGCCCAGGGTTTCCAAATCAAGGAATTGAAGTTT
Reverse complement sequence
AAACTTCAATTCCTTGATTTGGAAACCCTGGGCGCCGGGGAAATGCAAATTTCATGCTTGGCTCATCATTCAGAACAGAGTCTGGACTTTAGACCGGCTT[G/A]
CGACCAGGGGATGGCAGAACAATGGTTGTTGCCCTCTTTGCCGCCGCGAGACTGAGACGGCATTGCACCACGTTGCCACTTGTAGATACACCAAGAGGAT
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 | 31.10% | 0.20% | 5.31% | 63.46% | NA |
| All Indica | 2759 | 16.00% | 0.00% | 6.34% | 77.67% | NA |
| All Japonica | 1512 | 43.40% | 0.50% | 4.03% | 52.05% | NA |
| Aus | 269 | 89.20% | 0.00% | 2.97% | 7.81% | NA |
| Indica I | 595 | 8.60% | 0.00% | 4.03% | 87.39% | NA |
| Indica II | 465 | 13.30% | 0.00% | 3.66% | 83.01% | NA |
| Indica III | 913 | 20.40% | 0.00% | 10.08% | 69.55% | NA |
| Indica Intermediate | 786 | 18.10% | 0.00% | 5.34% | 76.59% | NA |
| Temperate Japonica | 767 | 60.80% | 0.00% | 1.56% | 37.68% | NA |
| Tropical Japonica | 504 | 25.80% | 0.20% | 7.74% | 66.27% | NA |
| Japonica Intermediate | 241 | 24.90% | 2.90% | 4.15% | 68.05% | NA |
| VI/Aromatic | 96 | 83.30% | 0.00% | 4.17% | 12.50% | NA |
| Intermediate | 90 | 56.70% | 0.00% | 3.33% | 40.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218480608 | C -> DEL | LOC_Os12g30780.1 | N | frameshift_variant | Average:6.277; most accessible tissue: Minghui63 young leaf, score: 11.521 | N | N | N | N |
| vg1218480608 | C -> T | LOC_Os12g30780.1 | missense_variant ; p.Ala135Thr; MODERATE | nonsynonymous_codon ; A135T | Average:6.277; most accessible tissue: Minghui63 young leaf, score: 11.521 | benign  |
0.567 |
TOLERATED | 0.07 |