Search for Variation information by Variation ID:
Detailed information for vg1105159988:
| Variant ID: vg1105159988 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5159988 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 47. )
Flanking Sequence (100 bp) in Reference Genome:
GGCCGAAGCTGCCACACCGGAACCGGAGGGGTTCCAGGTCCATGCCTCTTCCTTACGAGCCACTCGGTCCGCGAGCTGAAAAAGCTCCGCGGTAGTCTGG[A/G]
GCTCTTTGGAGGCGATCTTTTCGATCATGCGGTTGTGCCGCACACCCCCCCTGAACGCGTAGATCACCGCGTGTGCAGGGATGCATGGTATGGTGTTGCA
Reverse complement sequence
TGCAACACCATACCATGCATCCCTGCACACGCGGTGATCTACGCGTTCAGGGGGGGTGTGCGGCACAACCGCATGATCGAAAAGATCGCCTCCAAAGAGC[T/C]
CCAGACTACCGCGGAGCTTTTTCAGCTCGCGGACCGAGTGGCTCGTAAGGAAGAGGCATGGACCTGGAACCCCTCCGGTTCCGGTGTGGCAGCTTCGGCC
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 | 12.80% | 10.70% | 8.48% | 67.99% | NA |
| All Indica | 2759 | 6.50% | 1.20% | 6.16% | 86.15% | NA |
| All Japonica | 1512 | 27.20% | 29.80% | 13.69% | 29.23% | NA |
| Aus | 269 | 0.00% | 1.10% | 1.49% | 97.40% | NA |
| Indica I | 595 | 1.50% | 2.20% | 3.53% | 92.77% | NA |
| Indica II | 465 | 2.60% | 1.10% | 1.94% | 94.41% | NA |
| Indica III | 913 | 7.00% | 0.30% | 9.42% | 83.24% | NA |
| Indica Intermediate | 786 | 12.10% | 1.40% | 6.87% | 79.64% | NA |
| Temperate Japonica | 767 | 8.60% | 35.20% | 21.38% | 34.81% | NA |
| Tropical Japonica | 504 | 59.70% | 14.30% | 4.17% | 21.83% | NA |
| Japonica Intermediate | 241 | 18.70% | 45.20% | 9.13% | 26.97% | NA |
| VI/Aromatic | 96 | 2.10% | 5.20% | 12.50% | 80.21% | NA |
| Intermediate | 90 | 14.40% | 15.60% | 8.89% | 61.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105159988 | A -> DEL | LOC_Os11g09660.1 | N | frameshift_variant | Average:6.36; most accessible tissue: Callus, score: 13.429 | N | N | N | N |
| vg1105159988 | A -> G | LOC_Os11g09660.1 | missense_variant ; p.Leu378Pro; MODERATE | nonsynonymous_codon ; L378P | Average:6.36; most accessible tissue: Callus, score: 13.429 | benign  |
-0.576 |
TOLERATED | 1.00 |