Search for Variation information by Variation ID:
Detailed information for vg0142999845:
| Variant ID: vg0142999845 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 42999845 |
| 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:
GCTCCTGGCGTCGTCGGACAAGCGGGCAAAGGGCCAACTCCGGTCGTCAGGGGCCTTAGGCCTCCGTTCGGCTCGGGGGCCTCTTCTCCCTGCTCTTTCC[C/T]
GGGTCGAGTCAGCACAGGGTTAGCCTCGGGGTCAAAGGGCGATAGGTGCGGCCTTCCCACAGTGGCCTCAGGGCCTTCCTGGGGGTCGGGGGCTCCTAGC
Reverse complement sequence
GCTAGGAGCCCCCGACCCCCAGGAAGGCCCTGAGGCCACTGTGGGAAGGCCGCACCTATCGCCCTTTGACCCCGAGGCTAACCCTGTGCTGACTCGACCC[G/A]
GGAAAGAGCAGGGAGAAGAGGCCCCCGAGCCGAACGGAGGCCTAAGGCCCCTGACGACCGGAGTTGGCCCTTTGCCCGCTTGTCCGACGACGCCAGGAGC
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 | 12.60% | 0.20% | 9.48% | 77.72% | NA |
| All Indica | 2759 | 6.20% | 0.30% | 11.34% | 82.17% | NA |
| All Japonica | 1512 | 21.00% | 0.00% | 4.03% | 75.00% | NA |
| Aus | 269 | 32.30% | 0.00% | 15.24% | 52.42% | NA |
| Indica I | 595 | 3.50% | 0.00% | 4.54% | 91.93% | NA |
| Indica II | 465 | 3.00% | 0.00% | 6.45% | 90.54% | NA |
| Indica III | 913 | 9.30% | 0.80% | 19.28% | 70.65% | NA |
| Indica Intermediate | 786 | 6.40% | 0.30% | 10.18% | 83.21% | NA |
| Temperate Japonica | 767 | 38.70% | 0.00% | 0.39% | 60.89% | NA |
| Tropical Japonica | 504 | 1.20% | 0.00% | 10.12% | 88.69% | NA |
| Japonica Intermediate | 241 | 5.80% | 0.00% | 2.90% | 91.29% | NA |
| VI/Aromatic | 96 | 4.20% | 0.00% | 23.96% | 71.88% | NA |
| Intermediate | 90 | 18.90% | 1.10% | 11.11% | 68.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0142999845 | C -> T | LOC_Os01g74230.1 | missense_variant ; p.Gly1053Arg; MODERATE | nonsynonymous_codon ; G1053R | Average:4.687; most accessible tissue: Zhenshan97 flower, score: 9.663 | benign  |
0.975 |
DELETERIOUS | 0.04 |
| vg0142999845 | C -> DEL | LOC_Os01g74230.1 | N | frameshift_variant | Average:4.687; most accessible tissue: Zhenshan97 flower, score: 9.663 | N | N | N | N |