Search for Variation information by Variation ID:
Detailed information for vg0915031657:
| Variant ID: vg0915031657 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 15031657 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 80. )
Flanking Sequence (100 bp) in Reference Genome:
ACTGGTTCTACACCCCCCTCGCCAATGAAACGCGCCTCCGACTTCCAAGCCAGCCCCCGGCGCAGGTCTCCAGCTGGCGGGCGCCGGTAGATCTGGGGGA[G/T]
GACTACGACGCCGTCCTCGATCGCCTGGCGGGCCTGCGATCCCAGGGGCTCACCGGGGCCATGGTGTACGGCGATTACCTCCGTCGCCGGATTGCGCCGC
Reverse complement sequence
GCGGCGCAATCCGGCGACGGAGGTAATCGCCGTACACCATGGCCCCGGTGAGCCCCTGGGATCGCAGGCCCGCCAGGCGATCGAGGACGGCGTCGTAGTC[C/A]
TCCCCCAGATCTACCGGCGCCCGCCAGCTGGAGACCTGCGCCGGGGGCTGGCTTGGAAGTCGGAGGCGCGTTTCATTGGCGAGGGGGGTGTAGAACCAGT
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 | 13.10% | 0.10% | 1.48% | 85.27% | NA |
| All Indica | 2759 | 0.40% | 0.20% | 1.63% | 97.79% | NA |
| All Japonica | 1512 | 38.90% | 0.00% | 0.00% | 61.11% | NA |
| Aus | 269 | 0.00% | 0.40% | 9.29% | 90.33% | NA |
| Indica I | 595 | 0.30% | 0.00% | 1.51% | 98.15% | NA |
| Indica II | 465 | 0.90% | 0.20% | 1.72% | 97.20% | NA |
| Indica III | 913 | 0.00% | 0.30% | 1.75% | 97.92% | NA |
| Indica Intermediate | 786 | 0.60% | 0.10% | 1.53% | 97.71% | NA |
| Temperate Japonica | 767 | 66.50% | 0.00% | 0.00% | 33.51% | NA |
| Tropical Japonica | 504 | 4.00% | 0.00% | 0.00% | 96.03% | NA |
| Japonica Intermediate | 241 | 24.10% | 0.00% | 0.00% | 75.93% | NA |
| VI/Aromatic | 96 | 6.20% | 0.00% | 0.00% | 93.75% | NA |
| Intermediate | 90 | 16.70% | 0.00% | 0.00% | 83.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0915031657 | G -> DEL | LOC_Os09g25110.1 | N | frameshift_variant | Average:7.723; most accessible tissue: Minghui63 root, score: 17.665 | N | N | N | N |
| vg0915031657 | G -> T | LOC_Os09g25110.1 | missense_variant ; p.Glu121Asp; MODERATE | nonsynonymous_codon ; E121D | Average:7.723; most accessible tissue: Minghui63 root, score: 17.665 | benign  |
0.704 |
TOLERATED | 1.00 |