Search for Variation information by Variation ID:
Detailed information for vg0101920425:
| Variant ID: vg0101920425 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 1920425 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 304. )
Flanking Sequence (100 bp) in Reference Genome:
GCCATAGACAAGAGTACCGACCCAATCCCACCTACGGCCGGAACCCCCGGGACAGGCAGGCAGGACTGAGCCCCTAGCAGCAGGACACCGGCCCTGTGCC[A/C]
TGACATCTCGACTACCGGGCCGCAGCTCGTGTAGCCTTCATTTGCCCTGGAGAATGTCCATCGACCCCCGACTTCATCCATCTCCATCCGTGTACTTTTG
Reverse complement sequence
CAAAAGTACACGGATGGAGATGGATGAAGTCGGGGGTCGATGGACATTCTCCAGGGCAAATGAAGGCTACACGAGCTGCGGCCCGGTAGTCGAGATGTCA[T/G]
GGCACAGGGCCGGTGTCCTGCTGCTAGGGGCTCAGTCCTGCCTGCCTGTCCCGGGGGTTCCGGCCGTAGGTGGGATTGGGTCGGTACTCTTGTCTATGGC
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 90.60% | 0.00% | 1.25% | 8.13% | NA |
| All Indica | 2759 | 94.10% | 0.10% | 1.74% | 4.10% | NA |
| All Japonica | 1512 | 81.70% | 0.00% | 0.60% | 17.66% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.00% | 0.37% | NA |
| Indica I | 595 | 84.70% | 0.00% | 3.36% | 11.93% | NA |
| Indica II | 465 | 94.00% | 0.00% | 3.23% | 2.80% | NA |
| Indica III | 913 | 99.50% | 0.20% | 0.22% | 0.11% | NA |
| Indica Intermediate | 786 | 95.00% | 0.00% | 1.40% | 3.56% | NA |
| Temperate Japonica | 767 | 89.00% | 0.00% | 0.13% | 10.82% | NA |
| Tropical Japonica | 504 | 79.00% | 0.00% | 0.79% | 20.24% | NA |
| Japonica Intermediate | 241 | 64.30% | 0.00% | 1.66% | 34.02% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 0.00% | 1.11% | 3.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0101920425 | A -> DEL | LOC_Os01g04310.1 | N | frameshift_variant | Average:7.607; most accessible tissue: Callus, score: 11.73 | N | N | N | N |
| vg0101920425 | A -> C | LOC_Os01g04310.1 | missense_variant ; p.Trp3Gly; MODERATE | nonsynonymous_codon ; W3G | Average:7.607; most accessible tissue: Callus, score: 11.73 | benign  |
1.489 |
DELETERIOUS | 0.00 |