Search for Variation information by Variation ID:
Detailed information for vg0139513555:
| Variant ID: vg0139513555 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 39513555 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 254. )
Flanking Sequence (100 bp) in Reference Genome:
GGGTATCCTCGTTCCATACTCCCAAACTGCAACTCTCCTATCGCTCGCAGAATGCCAGCGTGCCTATCATGTATCAGGCATACATTTGGCCTCATACCAA[C/T]
AACTTTTGTTTTAACCAATTTCAGGAACCAGTACCAGCTGTCGGTATTCTCACTCTCAACAAAAGCAAATGCCAAGGGCAATACCTGATTGTTCCCATCT
Reverse complement sequence
AGATGGGAACAATCAGGTATTGCCCTTGGCATTTGCTTTTGTTGAGAGTGAGAATACCGACAGCTGGTACTGGTTCCTGAAATTGGTTAAAACAAAAGTT[G/A]
TTGGTATGAGGCCAAATGTATGCCTGATACATGATAGGCACGCTGGCATTCTGCGAGCGATAGGAGAGTTGCAGTTTGGGAGTATGGAACGAGGATACCC
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 | 26.70% | 0.10% | 0.87% | 72.34% | NA |
| All Indica | 2759 | 2.20% | 0.20% | 1.27% | 96.27% | NA |
| All Japonica | 1512 | 74.50% | 0.00% | 0.00% | 25.46% | NA |
| Aus | 269 | 2.20% | 0.00% | 0.74% | 97.03% | NA |
| Indica I | 595 | 2.70% | 0.00% | 1.01% | 96.30% | NA |
| Indica II | 465 | 1.10% | 0.00% | 0.00% | 98.92% | NA |
| Indica III | 913 | 2.20% | 0.10% | 0.66% | 97.04% | NA |
| Indica Intermediate | 786 | 2.70% | 0.60% | 2.93% | 93.77% | NA |
| Temperate Japonica | 767 | 97.10% | 0.00% | 0.00% | 2.87% | NA |
| Tropical Japonica | 504 | 52.00% | 0.00% | 0.00% | 48.02% | NA |
| Japonica Intermediate | 241 | 49.80% | 0.00% | 0.00% | 50.21% | NA |
| VI/Aromatic | 96 | 25.00% | 0.00% | 2.08% | 72.92% | NA |
| Intermediate | 90 | 45.60% | 0.00% | 2.22% | 52.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0139513555 | C -> T | LOC_Os01g67990.1 | missense_variant ; p.Val447Ile; MODERATE | nonsynonymous_codon ; V447I | Average:5.54; most accessible tissue: Callus, score: 16.271 | benign  |
0.494 |
DELETERIOUS | 0.01 |
| vg0139513555 | C -> DEL | LOC_Os01g67990.1 | N | frameshift_variant | Average:5.54; most accessible tissue: Callus, score: 16.271 | N | N | N | N |