Search for Variation information by Variation ID:
Detailed information for vg0139513874:
| Variant ID: vg0139513874 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 39513874 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CCTTTACAGCACACTCTTGCCAGGATGTTCAATTGAGGGGAATTTCTTCACTTCGTAAGAGCTCCCAGGGTTTCTTTCCTCGATAACATCAAGCAGGCGT[G/A]
GCAAATTGTCATATGAGGCTTTGTAAGTTCCAAATCTCATCTCTATTATTTTCTGTTTGGCCCTCCAGGCCTTGGCATAGCTAATAGTATACTTGTATGT
Reverse complement sequence
ACATACAAGTATACTATTAGCTATGCCAAGGCCTGGAGGGCCAAACAGAAAATAATAGAGATGAGATTTGGAACTTACAAAGCCTCATATGACAATTTGC[C/T]
ACGCCTGCTTGATGTTATCGAGGAAAGAAACCCTGGGAGCTCTTACGAAGTGAAGAAATTCCCCTCAATTGAACATCCTGGCAAGAGTGTGCTGTAAAGG
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 | 26.30% | 1.00% | 1.18% | 71.52% | NA |
| All Indica | 2759 | 2.70% | 0.40% | 1.81% | 95.11% | NA |
| All Japonica | 1512 | 74.80% | 0.30% | 0.20% | 24.74% | NA |
| Aus | 269 | 0.00% | 2.20% | 0.74% | 97.03% | NA |
| Indica I | 595 | 3.50% | 0.00% | 2.86% | 93.61% | NA |
| Indica II | 465 | 0.90% | 0.00% | 0.00% | 99.14% | NA |
| Indica III | 913 | 1.20% | 1.00% | 1.97% | 95.84% | NA |
| Indica Intermediate | 786 | 4.80% | 0.30% | 1.91% | 93.00% | NA |
| Temperate Japonica | 767 | 97.40% | 0.00% | 0.00% | 2.61% | NA |
| Tropical Japonica | 504 | 52.60% | 0.00% | 0.40% | 47.02% | NA |
| Japonica Intermediate | 241 | 49.40% | 1.70% | 0.41% | 48.55% | NA |
| VI/Aromatic | 96 | 1.00% | 22.90% | 1.04% | 75.00% | NA |
| Intermediate | 90 | 41.10% | 4.40% | 0.00% | 54.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0139513874 | G -> A | LOC_Os01g67990.1 | missense_variant ; p.Pro372Leu; MODERATE | nonsynonymous_codon ; P372L | Average:6.876; most accessible tissue: Callus, score: 26.099 | possibly damaging  |
1.972 |
DELETERIOUS | 0.01 |
| vg0139513874 | G -> DEL | LOC_Os01g67990.1 | N | frameshift_variant | Average:6.876; most accessible tissue: Callus, score: 26.099 | N | N | N | N |