Search for Variation information by Variation ID:
Detailed information for vg0424677770:
| Variant ID: vg0424677770 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 24677770 |
| 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: 127. )
Flanking Sequence (100 bp) in Reference Genome:
CAGGTCGATTCGTCCTGTGTTTGCATGGCGTCCATACTCTGTGATCCTACCTGCCCCGTTGAGGCGCAGCTGCTACGGTTTCCTGACGGGCTCACCATTG[C/T]
AGGAGGAATGGTCGGCTGGGGATCATGGGACCGATGTGCGGCCATGCGTTCATCAACCTTCCTTGCCACCTCCTCTTGCATGTTGAGTTCGTAGCTCGAT
Reverse complement sequence
ATCGAGCTACGAACTCAACATGCAAGAGGAGGTGGCAAGGAAGGTTGATGAACGCATGGCCGCACATCGGTCCCATGATCCCCAGCCGACCATTCCTCCT[G/A]
CAATGGTGAGCCCGTCAGGAAACCGTAGCAGCTGCGCCTCAACGGGGCAGGTAGGATCACAGAGTATGGACGCCATGCAAACACAGGACGAATCGACCTG
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 | 12.30% | 0.70% | 10.24% | 76.77% | NA |
| All Indica | 2759 | 1.00% | 1.20% | 3.30% | 94.49% | NA |
| All Japonica | 1512 | 33.90% | 0.10% | 19.64% | 46.43% | NA |
| Aus | 269 | 1.90% | 0.00% | 12.64% | 85.50% | NA |
| Indica I | 595 | 1.00% | 0.20% | 3.87% | 94.96% | NA |
| Indica II | 465 | 0.90% | 0.60% | 1.94% | 96.56% | NA |
| Indica III | 913 | 0.90% | 2.50% | 3.07% | 93.54% | NA |
| Indica Intermediate | 786 | 1.10% | 0.90% | 3.94% | 94.02% | NA |
| Temperate Japonica | 767 | 60.60% | 0.10% | 16.56% | 22.69% | NA |
| Tropical Japonica | 504 | 1.00% | 0.00% | 24.21% | 74.80% | NA |
| Japonica Intermediate | 241 | 17.40% | 0.00% | 19.92% | 62.66% | NA |
| VI/Aromatic | 96 | 30.20% | 0.00% | 51.04% | 18.75% | NA |
| Intermediate | 90 | 6.70% | 0.00% | 14.44% | 78.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0424677770 | C -> DEL | LOC_Os04g41599.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0424677770 | C -> T | LOC_Os04g41599.1 | missense_variant ; p.Ala1318Thr; MODERATE | nonsynonymous_codon ; A1318T | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
0.723 |
TOLERATED | 0.05 |