Search for Variation information by Variation ID:
Detailed information for vg1212666385:
| Variant ID: vg1212666385 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 12666385 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GCCACTCCAAATTGGTGAATCTTCTTCCGCTGGTCAAGGACAGTCGCAACTGTTGAACATCGGTGGTGAGATCAAATTAGAGACTAATGAAAGTAATGAA[G/A]
TAAACATCGAGCAAGCTAATCAGCCGGTGCCAGTTCAGCAGGATCAGTCTCAGGAGAATAACAGTAGTGGAAGGGAGCAGTAGGTATGTTTCAACTGTTA
Reverse complement sequence
TAACAGTTGAAACATACCTACTGCTCCCTTCCACTACTGTTATTCTCCTGAGACTGATCCTGCTGAACTGGCACCGGCTGATTAGCTTGCTCGATGTTTA[C/T]
TTCATTACTTTCATTAGTCTCTAATTTGATCTCACCACCGATGTTCAACAGTTGCGACTGTCCTTGACCAGCGGAAGAAGATTCACCAATTTGGAGTGGC
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 30.50% | 0.10% | 14.18% | 55.18% | NA |
| All Indica | 2759 | 26.50% | 0.00% | 17.80% | 55.67% | NA |
| All Japonica | 1512 | 44.30% | 0.00% | 1.19% | 54.50% | NA |
| Aus | 269 | 1.90% | 1.90% | 51.67% | 44.61% | NA |
| Indica I | 595 | 16.50% | 0.00% | 6.22% | 77.31% | NA |
| Indica II | 465 | 21.50% | 0.00% | 12.47% | 66.02% | NA |
| Indica III | 913 | 36.10% | 0.10% | 28.92% | 34.83% | NA |
| Indica Intermediate | 786 | 25.80% | 0.00% | 16.79% | 57.38% | NA |
| Temperate Japonica | 767 | 77.70% | 0.00% | 0.26% | 22.03% | NA |
| Tropical Japonica | 504 | 3.00% | 0.00% | 2.98% | 94.05% | NA |
| Japonica Intermediate | 241 | 24.50% | 0.00% | 0.41% | 75.10% | NA |
| VI/Aromatic | 96 | 7.30% | 0.00% | 12.50% | 80.21% | NA |
| Intermediate | 90 | 32.20% | 0.00% | 11.11% | 56.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1212666385 | G -> DEL | LOC_Os12g22430.1 | N | frameshift_variant | Average:5.218; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg1212666385 | G -> A | LOC_Os12g22430.1 | missense_variant ; p.Val284Ile; MODERATE | nonsynonymous_codon ; V284I | Average:5.218; most accessible tissue: Zhenshan97 panicle, score: 16.188 | benign  |
1.068 |
TOLERATED | 1.00 |