Search for Variation information by Variation ID:
Detailed information for vg0128477180:
| Variant ID: vg0128477180 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 28477180 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 90. )
Flanking Sequence (100 bp) in Reference Genome:
TGCAATGGTTGCGATGAAGCCTGGAATGTATCTGGCCGGGGCTGACGTGCCAACTCCAGGAGTTCCCACGCCGGCTCCGGCTAGGGACGAGTGCCTGGAG[G/A]
CTCTCATCATTCCGACGGGATGGGGCGAGGCGTGTGTCAGGCCGCCTGTTGCCCCCTAACCCGCGATCTGACCGGTCTGTGACCGGTCACACACTGCGAC
Reverse complement sequence
GTCGCAGTGTGTGACCGGTCACAGACCGGTCAGATCGCGGGTTAGGGGGCAACAGGCGGCCTGACACACGCCTCGCCCCATCCCGTCGGAATGATGAGAG[C/T]
CTCCAGGCACTCGTCCCTAGCCGGAGCCGGCGTGGGAACTCCTGGAGTTGGCACGTCAGCCCCGGCCAGATACATTCCAGGCTTCATCGCAACCATTGCA
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 29.10% | 3.90% | 2.14% | 64.90% | NA |
| All Indica | 2759 | 2.50% | 0.60% | 1.56% | 95.36% | NA |
| All Japonica | 1512 | 83.30% | 10.40% | 2.91% | 3.44% | NA |
| Aus | 269 | 0.70% | 0.00% | 3.72% | 95.54% | NA |
| Indica I | 595 | 4.40% | 0.00% | 3.36% | 92.27% | NA |
| Indica II | 465 | 2.40% | 1.90% | 0.22% | 95.48% | NA |
| Indica III | 913 | 1.20% | 0.00% | 1.20% | 97.59% | NA |
| Indica Intermediate | 786 | 2.70% | 0.90% | 1.40% | 95.04% | NA |
| Temperate Japonica | 767 | 99.50% | 0.30% | 0.00% | 0.26% | NA |
| Tropical Japonica | 504 | 55.20% | 28.60% | 8.13% | 8.13% | NA |
| Japonica Intermediate | 241 | 90.50% | 4.60% | 1.24% | 3.73% | NA |
| VI/Aromatic | 96 | 14.60% | 0.00% | 1.04% | 84.38% | NA |
| Intermediate | 90 | 32.20% | 13.30% | 3.33% | 51.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0128477180 | G -> A | LOC_Os01g49500.1 | missense_variant ; p.Ala90Thr; MODERATE | nonsynonymous_codon ; A90T | Average:5.814; most accessible tissue: Callus, score: 15.328 | benign  |
0.382 |
DELETERIOUS | 0.04 |
| vg0128477180 | G -> DEL | LOC_Os01g49500.1 | N | frameshift_variant | Average:5.814; most accessible tissue: Callus, score: 15.328 | N | N | N | N |