Search for Variation information by Variation ID:
Detailed information for vg0135357941:
| Variant ID: vg0135357941 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 35357941 |
| 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: 272. )
Flanking Sequence (100 bp) in Reference Genome:
TCTGACTCATCCATATCATTTCTGATGCGTCTAGTTTGGCGTCGACCCTTTTTCACCCTTAACTTAGATGGATCTGGAATGTAAAAAACTTGGGCACTCA[G/T]
CGTTGTGTAAGATCCTGAGATCCCGAACCCATATATCTCCTCACTCCATGTATGAAAGATTGCTTCTTTCCTGAAATAATTTGAGACGTACACATTGGGA
Reverse complement sequence
TCCCAATGTGTACGTCTCAAATTATTTCAGGAAAGAAGCAATCTTTCATACATGGAGTGAGGAGATATATGGGTTCGGGATCTCAGGATCTTACACAACG[C/A]
TGAGTGCCCAAGTTTTTTACATTCCAGATCCATCTAAGTTAAGGGTGAAAAAGGGTCGACGCCAAACTAGACGCATCAGAAATGATATGGATGAGTCAGA
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 | 24.70% | 0.10% | 2.05% | 73.13% | NA |
| All Indica | 2759 | 2.20% | 0.10% | 1.23% | 96.41% | NA |
| All Japonica | 1512 | 64.20% | 0.10% | 3.51% | 32.28% | NA |
| Aus | 269 | 0.40% | 1.10% | 2.23% | 96.28% | NA |
| Indica I | 595 | 4.00% | 0.00% | 1.01% | 94.96% | NA |
| Indica II | 465 | 0.40% | 0.00% | 1.08% | 98.49% | NA |
| Indica III | 913 | 0.80% | 0.00% | 1.86% | 97.37% | NA |
| Indica Intermediate | 786 | 3.70% | 0.40% | 0.76% | 95.17% | NA |
| Temperate Japonica | 767 | 57.10% | 0.00% | 0.52% | 42.37% | NA |
| Tropical Japonica | 504 | 65.90% | 0.20% | 9.33% | 24.60% | NA |
| Japonica Intermediate | 241 | 83.00% | 0.00% | 0.83% | 16.18% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 0.00% | 7.29% | NA |
| Intermediate | 90 | 48.90% | 0.00% | 4.44% | 46.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0135357941 | G -> T | LOC_Os01g61090.1 | missense_variant ; p.Leu802Met; MODERATE | nonsynonymous_codon ; L802M | Average:5.003; most accessible tissue: Zhenshan97 root, score: 10.511 | probably damaging  |
2.14 |
TOLERATED | 0.22 |
| vg0135357941 | G -> DEL | LOC_Os01g61090.1 | N | frameshift_variant | Average:5.003; most accessible tissue: Zhenshan97 root, score: 10.511 | N | N | N | N |