Search for Variation information by Variation ID:
Detailed information for vg1218480799:
| Variant ID: vg1218480799 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18480799 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ATTGAAGTTTGTACTCGGCGCCCCGCAGCACTGCGCATGGTAAGCCGAGGAGGCCGTGTAGTGCCCGTTGTTTGTGAACTTCCAAGTAATCTGATCCGGT[T/C]
CTCCAACATCTAAGTGCACATTTCGGACCGCTTCCCACAGTGCGACTAGCTGTTCGACGAGGTCGACTGCGATAGATGATTGTGAATCAAGCTTAAAATC
Reverse complement sequence
GATTTTAAGCTTGATTCACAATCATCTATCGCAGTCGACCTCGTCGAACAGCTAGTCGCACTGTGGGAAGCGGTCCGAAATGTGCACTTAGATGTTGGAG[A/G]
ACCGGATCAGATTACTTGGAAGTTCACAAACAACGGGCACTACACGGCCTCCTCGGCTTACCATGCGCAGTGCTGCGGGGCGCCGAGTACAAACTTCAAT
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 | 13.80% | 0.30% | 5.61% | 80.32% | NA |
| All Indica | 2759 | 3.00% | 0.40% | 3.84% | 92.71% | NA |
| All Japonica | 1512 | 35.10% | 0.00% | 0.26% | 64.68% | NA |
| Aus | 269 | 3.70% | 0.00% | 52.04% | 44.24% | NA |
| Indica I | 595 | 3.20% | 0.20% | 2.86% | 93.78% | NA |
| Indica II | 465 | 3.40% | 0.60% | 2.80% | 93.12% | NA |
| Indica III | 913 | 2.20% | 0.50% | 4.93% | 92.33% | NA |
| Indica Intermediate | 786 | 3.60% | 0.40% | 3.94% | 92.11% | NA |
| Temperate Japonica | 767 | 59.70% | 0.00% | 0.39% | 39.90% | NA |
| Tropical Japonica | 504 | 3.20% | 0.00% | 0.20% | 96.63% | NA |
| Japonica Intermediate | 241 | 23.20% | 0.00% | 0.00% | 76.76% | NA |
| VI/Aromatic | 96 | 4.20% | 0.00% | 8.33% | 87.50% | NA |
| Intermediate | 90 | 28.90% | 0.00% | 7.78% | 63.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218480799 | T -> C | LOC_Os12g30780.1 | missense_variant ; p.Glu71Gly; MODERATE | nonsynonymous_codon ; E71G | Average:6.619; most accessible tissue: Callus, score: 17.876 | possibly damaging  |
1.636 |
TOLERATED | 0.10 |
| vg1218480799 | T -> DEL | LOC_Os12g30780.1 | N | frameshift_variant | Average:6.619; most accessible tissue: Callus, score: 17.876 | N | N | N | N |