Search for Variation information by Variation ID:
Detailed information for vg0108239558:
| Variant ID: vg0108239558 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 8239558 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 281. )
Flanking Sequence (100 bp) in Reference Genome:
CTTCACCGACCGGCTTGCCTTCGCCGCCGCCGATTGGTGCCTCCGTCTACACGGCTGGCCTGTTATAACGCCAACTGATGCTATCTTCTTCACGGCTGGC[T/C]
ACATCGCTGTCACTACTAATAGGCATCAGTATCTTCAACACAAGCTGCCTACGTTTGCCATGGCTGCCGACTGGTTTCTTCACTTCCATGGCTGCATGAT
Reverse complement sequence
ATCATGCAGCCATGGAAGTGAAGAAACCAGTCGGCAGCCATGGCAAACGTAGGCAGCTTGTGTTGAAGATACTGATGCCTATTAGTAGTGACAGCGATGT[A/G]
GCCAGCCGTGAAGAAGATAGCATCAGTTGGCGTTATAACAGGCCAGCCGTGTAGACGGAGGCACCAATCGGCGGCGGCGAAGGCAAGCCGGTCGGTGAAG
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.40% | 0.10% | 1.46% | 0.00% | NA |
| All Indica | 2759 | 98.90% | 0.30% | 0.80% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.07% | 0.00% | NA |
| Aus | 269 | 82.90% | 0.00% | 17.10% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.17% | 0.00% | NA |
| Indica II | 465 | 99.40% | 0.00% | 0.65% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.00% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 96.90% | 0.90% | 2.16% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0108239558 | T -> C | LOC_Os01g14730.1 | missense_variant ; p.Tyr215His; MODERATE | nonsynonymous_codon ; Y215H | Average:46.991; most accessible tissue: Zhenshan97 flag leaf, score: 70.425 | possibly damaging  |
1.642 |
TOLERATED | 0.29 |