Search for Variation information by Variation ID:
Detailed information for vg0710350879:
| Variant ID: vg0710350879 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 10350879 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ATACATGTACGAACTCGGTAAACCGCTTGTCAAGCCTGAGCTGCTGCAGTCCCTACCCACACAAATGTACAAGTTCCATCAGCTGTACATGGAGATGAGC[G/A]
CCACCGGTAGAGAGATGATCGGAGCGAGGATCAAGGACACTGACTTCTTGCAAGGAGATGACATTCTCTGGATCAATTTCAGGGGAATCTACGAACTATA
Reverse complement sequence
TATAGTTCGTAGATTCCCCTGAAATTGATCCAGAGAATGTCATCTCCTTGCAAGAAGTCAGTGTCCTTGATCCTCGCTCCGATCATCTCTCTACCGGTGG[C/T]
GCTCATCTCCATGTACAGCTGATGGAACTTGTACATTTGTGTGGGTAGGGACTGCAGCAGCTCAGGCTTGACAAGCGGTTTACCGAGTTCGTACATGTAT
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 | 30.80% | 0.40% | 7.07% | 61.72% | NA |
| All Indica | 2759 | 6.10% | 0.00% | 6.78% | 87.10% | NA |
| All Japonica | 1512 | 73.30% | 1.20% | 9.13% | 16.34% | NA |
| Aus | 269 | 50.60% | 0.00% | 0.74% | 48.70% | NA |
| Indica I | 595 | 8.60% | 0.00% | 5.21% | 86.22% | NA |
| Indica II | 465 | 6.90% | 0.00% | 5.16% | 87.96% | NA |
| Indica III | 913 | 3.60% | 0.00% | 6.24% | 90.14% | NA |
| Indica Intermediate | 786 | 6.70% | 0.00% | 9.54% | 83.72% | NA |
| Temperate Japonica | 767 | 62.20% | 0.00% | 13.95% | 23.86% | NA |
| Tropical Japonica | 504 | 85.90% | 3.60% | 0.20% | 10.32% | NA |
| Japonica Intermediate | 241 | 82.60% | 0.00% | 12.45% | 4.98% | NA |
| VI/Aromatic | 96 | 5.20% | 0.00% | 4.17% | 90.62% | NA |
| Intermediate | 90 | 41.10% | 1.10% | 3.33% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0710350879 | G -> DEL | LOC_Os07g17510.1 | N | frameshift_variant | Average:6.942; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| vg0710350879 | G -> A | LOC_Os07g17510.1 | missense_variant ; p.Ala751Thr; MODERATE | nonsynonymous_codon ; A751T | Average:6.942; most accessible tissue: Minghui63 panicle, score: 16.27 | benign  |
0.715 |
DELETERIOUS | 0.04 |