Search for Variation information by Variation ID:
Detailed information for vg1218480619:
| Variant ID: vg1218480619 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18480619 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GTATCTACAAGTGGCAACGTGGTGCAATGCCGTCTCAGTCTCGCGGCGGCAAAGAGGGCAACAACCATTGTTCTGCCATCCCCTGGTCGCAAGCCGGTCT[A/G]
AAGTCCAGACTCTGTTCTGAATGATGAGCCAAGCATGAAATTTGCATTTCCCCGGCGCCCAGGGTTTCCAAATCAAGGAATTGAAGTTTGTACTCGGCGC
Reverse complement sequence
GCGCCGAGTACAAACTTCAATTCCTTGATTTGGAAACCCTGGGCGCCGGGGAAATGCAAATTTCATGCTTGGCTCATCATTCAGAACAGAGTCTGGACTT[T/C]
AGACCGGCTTGCGACCAGGGGATGGCAGAACAATGGTTGTTGCCCTCTTTGCCGCCGCGAGACTGAGACGGCATTGCACCACGTTGCCACTTGTAGATAC
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 29.90% | 0.60% | 6.88% | 62.63% | NA |
| All Indica | 2759 | 12.80% | 0.70% | 9.89% | 76.62% | NA |
| All Japonica | 1512 | 45.80% | 0.10% | 2.65% | 51.46% | NA |
| Aus | 269 | 85.50% | 2.20% | 1.86% | 10.41% | NA |
| Indica I | 595 | 5.70% | 0.50% | 5.88% | 87.90% | NA |
| Indica II | 465 | 11.20% | 0.20% | 6.45% | 82.15% | NA |
| Indica III | 913 | 16.80% | 0.90% | 15.77% | 66.59% | NA |
| Indica Intermediate | 786 | 14.50% | 0.90% | 8.14% | 76.46% | NA |
| Temperate Japonica | 767 | 61.80% | 0.00% | 1.30% | 36.90% | NA |
| Tropical Japonica | 504 | 27.80% | 0.40% | 4.17% | 67.66% | NA |
| Japonica Intermediate | 241 | 32.40% | 0.00% | 3.73% | 63.90% | NA |
| VI/Aromatic | 96 | 88.50% | 0.00% | 2.08% | 9.38% | NA |
| Intermediate | 90 | 58.90% | 1.10% | 5.56% | 34.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218480619 | A -> DEL | LOC_Os12g30780.1 | N | frameshift_variant | Average:6.277; most accessible tissue: Minghui63 young leaf, score: 11.521 | N | N | N | N |
| vg1218480619 | A -> G | LOC_Os12g30780.1 | missense_variant ; p.Leu131Ser; MODERATE | nonsynonymous_codon ; L131S | Average:6.277; most accessible tissue: Minghui63 young leaf, score: 11.521 | possibly damaging  |
-1.62 |
TOLERATED | 1.00 |