Search for Variation information by Variation ID:
Detailed information for vg0415573926:
| Variant ID: vg0415573926 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 15573926 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 72. )
Flanking Sequence (100 bp) in Reference Genome:
AAGGAGTTCTGTAAAATTCTTGTCCGACCAGCCATTACTAGCCTTAAGCTTCATGAGTTCCAACACGCATGACAACTTACTGTGCTTCGACTTGCATCCA[T/G]
CATACAACGGCATCTGGCAATCTTCCACCAACTTACTAAACTTCTCATAATCTCTGTCGTTGTCCTCTGCGTCTTCAATGTCATGCAACATTGTAGATAG
Reverse complement sequence
CTATCTACAATGTTGCATGACATTGAAGACGCAGAGGACAACGACAGAGATTATGAGAAGTTTAGTAAGTTGGTGGAAGATTGCCAGATGCCGTTGTATG[A/C]
TGGATGCAAGTCGAAGCACAGTAAGTTGTCATGCGTGTTGGAACTCATGAAGCTTAAGGCTAGTAATGGCTGGTCGGACAAGAATTTTACAGAACTCCTT
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 0.20% | 0.00% | 41.79% | 57.96% | NA |
| All Indica | 2759 | 0.40% | 0.00% | 43.64% | 55.96% | NA |
| All Japonica | 1512 | 0.00% | 0.10% | 44.51% | 55.42% | NA |
| Aus | 269 | 0.00% | 0.00% | 3.35% | 96.65% | NA |
| Indica I | 595 | 0.50% | 0.00% | 33.45% | 66.05% | NA |
| Indica II | 465 | 1.50% | 0.00% | 35.27% | 63.23% | NA |
| Indica III | 913 | 0.00% | 0.00% | 57.17% | 42.83% | NA |
| Indica Intermediate | 786 | 0.10% | 0.00% | 40.59% | 59.29% | NA |
| Temperate Japonica | 767 | 0.00% | 0.10% | 29.47% | 70.40% | NA |
| Tropical Japonica | 504 | 0.00% | 0.00% | 62.70% | 37.30% | NA |
| Japonica Intermediate | 241 | 0.00% | 0.00% | 54.36% | 45.64% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 48.96% | 51.04% | NA |
| Intermediate | 90 | 0.00% | 0.00% | 46.67% | 53.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0415573926 | T -> DEL | LOC_Os04g26690.1 | N | frameshift_variant | Average:9.228; most accessible tissue: Minghui63 root, score: 21.615 | N | N | N | N |
| vg0415573926 | T -> G | LOC_Os04g26690.1 | missense_variant ; p.Asp211Ala; MODERATE | nonsynonymous_codon ; D211A | Average:9.228; most accessible tissue: Minghui63 root, score: 21.615 | possibly damaging  |
1.623 |
TOLERATED | 1.00 |