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Detailed information for vg0234180544:
| Variant ID: vg0234180544 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 34180544 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 309. )
Flanking Sequence (100 bp) in Reference Genome:
TCCTGTGCTATCAAAACTAGCACAGGATGTGTTGACGGTGCCCGTATCTTCGGTATCCTCCGAATCAGCCTTCAGTCTATGCGGAAGAATTATCGAGGAT[A/T]
GGAGAACAAGTCTGAGCAGCGATCATGTGGAAATACTATTAAGCGTCAAAGACTGGGAACTTGCTGCAGAACATACCCAATACACTGCTGACAACCAAGA
Reverse complement sequence
TCTTGGTTGTCAGCAGTGTATTGGGTATGTTCTGCAGCAAGTTCCCAGTCTTTGACGCTTAATAGTATTTCCACATGATCGCTGCTCAGACTTGTTCTCC[T/A]
ATCCTCGATAATTCTTCCGCATAGACTGAAGGCTGATTCGGAGGATACCGAAGATACGGGCACCGTCAACACATCCTGTGCTAGTTTTGATAGCACAGGA
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 39.50% | 12.00% | 7.02% | 41.52% | NA |
| All Indica | 2759 | 9.10% | 18.40% | 8.08% | 64.44% | NA |
| All Japonica | 1512 | 94.50% | 3.30% | 0.53% | 1.65% | NA |
| Aus | 269 | 39.40% | 0.00% | 29.00% | 31.60% | NA |
| Indica I | 595 | 2.70% | 16.10% | 5.21% | 75.97% | NA |
| Indica II | 465 | 11.60% | 8.60% | 4.09% | 75.70% | NA |
| Indica III | 913 | 9.70% | 25.10% | 11.83% | 53.34% | NA |
| Indica Intermediate | 786 | 11.60% | 18.20% | 8.27% | 61.96% | NA |
| Temperate Japonica | 767 | 97.70% | 0.00% | 0.39% | 1.96% | NA |
| Tropical Japonica | 504 | 89.70% | 9.70% | 0.40% | 0.20% | NA |
| Japonica Intermediate | 241 | 94.60% | 0.40% | 1.24% | 3.73% | NA |
| VI/Aromatic | 96 | 33.30% | 0.00% | 15.62% | 51.04% | NA |
| Intermediate | 90 | 54.40% | 8.90% | 8.89% | 27.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0234180544 | A -> T | LOC_Os02g55830.1 | missense_variant ; p.Arg509Trp; MODERATE | nonsynonymous_codon ; R509W | Average:7.023; most accessible tissue: Callus, score: 24.171 | benign  |
0.831 |
DELETERIOUS | 0.01 |
| vg0234180544 | A -> DEL | LOC_Os02g55830.1 | N | frameshift_variant | Average:7.023; most accessible tissue: Callus, score: 24.171 | N | N | N | N |