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Detailed information for vg1101256060:
| Variant ID: vg1101256060 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 1256060 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 268. )
Flanking Sequence (100 bp) in Reference Genome:
CTCTCTTTCCAGTATGTTCTATGCATTTTACTTGACTTATATTTGCCCAAAATGAGTCCGTTTGTTAACTAAATACAGGCAATGAGCCTTAGAAACTCTC[G/A]
GAACAGAGCAGGCTTAAAAATGCCTCATCGCACTGGAAGCAAACCCTTCAGAGAGATAATCTACAATATGGTATAAATAAAAGAATTATGTACATAATTT
Reverse complement sequence
AAATTATGTACATAATTCTTTTATTTATACCATATTGTAGATTATCTCTCTGAAGGGTTTGCTTCCAGTGCGATGAGGCATTTTTAAGCCTGCTCTGTTC[C/T]
GAGAGTTTCTAAGGCTCATTGCCTGTATTTAGTTAACAAACGGACTCATTTTGGGCAAATATAAGTCAAGTAAAATGCATAGAACATACTGGAAAGAGAG
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 | 44.80% | 21.00% | 3.43% | 30.77% | NA |
| All Indica | 2759 | 12.00% | 35.60% | 4.17% | 48.28% | NA |
| All Japonica | 1512 | 97.60% | 0.10% | 0.20% | 2.05% | NA |
| Aus | 269 | 75.80% | 0.40% | 4.83% | 18.96% | NA |
| Indica I | 595 | 15.80% | 1.80% | 6.39% | 75.97% | NA |
| Indica II | 465 | 7.10% | 36.10% | 3.87% | 52.90% | NA |
| Indica III | 913 | 7.40% | 60.90% | 1.75% | 29.90% | NA |
| Indica Intermediate | 786 | 17.30% | 31.30% | 5.47% | 45.93% | NA |
| Temperate Japonica | 767 | 98.20% | 0.30% | 0.13% | 1.43% | NA |
| Tropical Japonica | 504 | 97.40% | 0.00% | 0.20% | 2.38% | NA |
| Japonica Intermediate | 241 | 96.30% | 0.00% | 0.41% | 3.32% | NA |
| VI/Aromatic | 96 | 57.30% | 1.00% | 31.25% | 10.42% | NA |
| Intermediate | 90 | 57.80% | 7.80% | 1.11% | 33.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1101256060 | G -> A | LOC_Os11g03340.1 | missense_variant ; p.Arg269Gln; MODERATE | nonsynonymous_codon ; R269Q | Average:4.744; most accessible tissue: Callus, score: 7.517 | benign  |
0.107 |
TOLERATED | 0.62 |
| vg1101256060 | G -> DEL | LOC_Os11g03340.1 | N | frameshift_variant | Average:4.744; most accessible tissue: Callus, score: 7.517 | N | N | N | N |