Search for Variation information by Variation ID:
Detailed information for vg1212666289:
| Variant ID: vg1212666289 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 12666289 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 291. )
Flanking Sequence (100 bp) in Reference Genome:
TCGCCTTGAAGACAAGAAGAACAGGATGGATAACCGTAAAAGGAAAATGACTGTTTTCCAGGAGGCACAAGGTAGTAGCCAGAGGCAGCGTATCAAGCCA[C/T]
TCCAAATTGGTGAATCTTCTTCCGCTGGTCAAGGACAGTCGCAACTGTTGAACATCGGTGGTGAGATCAAATTAGAGACTAATGAAAGTAATGAAGTAAA
Reverse complement sequence
TTTACTTCATTACTTTCATTAGTCTCTAATTTGATCTCACCACCGATGTTCAACAGTTGCGACTGTCCTTGACCAGCGGAAGAAGATTCACCAATTTGGA[G/A]
TGGCTTGATACGCTGCCTCTGGCTACTACCTTGTGCCTCCTGGAAAACAGTCATTTTCCTTTTACGGTTATCCATCCTGTTCTTCTTGTCTTCAAGGCGA
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 | 81.50% | 0.30% | 1.48% | 16.72% | NA |
| All Indica | 2759 | 83.10% | 0.50% | 1.52% | 14.86% | NA |
| All Japonica | 1512 | 75.80% | 0.00% | 1.46% | 22.75% | NA |
| Aus | 269 | 95.90% | 0.00% | 0.37% | 3.72% | NA |
| Indica I | 595 | 70.30% | 0.30% | 2.69% | 26.72% | NA |
| Indica II | 465 | 82.60% | 1.10% | 1.29% | 15.05% | NA |
| Indica III | 913 | 91.20% | 0.40% | 0.55% | 7.78% | NA |
| Indica Intermediate | 786 | 83.60% | 0.50% | 1.91% | 13.99% | NA |
| Temperate Japonica | 767 | 84.60% | 0.00% | 0.26% | 15.12% | NA |
| Tropical Japonica | 504 | 68.80% | 0.00% | 2.78% | 28.37% | NA |
| Japonica Intermediate | 241 | 62.20% | 0.00% | 2.49% | 35.27% | NA |
| VI/Aromatic | 96 | 87.50% | 0.00% | 2.08% | 10.42% | NA |
| Intermediate | 90 | 78.90% | 0.00% | 3.33% | 17.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1212666289 | C -> DEL | LOC_Os12g22430.1 | N | frameshift_variant | Average:4.447; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1212666289 | C -> T | LOC_Os12g22430.1 | missense_variant ; p.Leu252Phe; MODERATE | nonsynonymous_codon ; L252F | Average:4.447; most accessible tissue: Minghui63 panicle, score: 7.125 | probably damaging  |
2.008 |
TOLERATED | 0.13 |