Search for Variation information by Variation ID:
Detailed information for vg1007671811:
| Variant ID: vg1007671811 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7671811 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CTTATCCTCGCTGAATAGCCCGATGGAACTTTAATATCCTTCAAGCATGATAACATTGCGATCTTCTCATCCTTCGACAGTGTGTGGCAGGCTGGAGGGA[C/A]
GTACACTTTACTTGTCTCTGCATCTCGTATGGGCTGGAGTTCGCTGCGAATATTCATGTCCTGTAGATCAAGGCGCGCGTTCAACCCGTCCTTTGTCTTC
Reverse complement sequence
GAAGACAAAGGACGGGTTGAACGCGCGCCTTGATCTACAGGACATGAATATTCGCAGCGAACTCCAGCCCATACGAGATGCAGAGACAAGTAAAGTGTAC[G/T]
TCCCTCCAGCCTGCCACACACTGTCGAAGGATGAGAAGATCGCAATGTTATCATGCTTGAAGGATATTAAAGTTCCATCGGGCTATTCAGCGAGGATAAG
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 13.50% | 0.10% | 7.72% | 78.67% | NA |
| All Indica | 2759 | 1.30% | 0.20% | 3.37% | 95.14% | NA |
| All Japonica | 1512 | 38.80% | 0.00% | 2.05% | 59.19% | NA |
| Aus | 269 | 0.40% | 0.00% | 73.98% | 25.65% | NA |
| Indica I | 595 | 0.80% | 0.00% | 0.34% | 98.82% | NA |
| Indica II | 465 | 1.50% | 0.00% | 1.29% | 97.20% | NA |
| Indica III | 913 | 1.20% | 0.50% | 4.16% | 94.09% | NA |
| Indica Intermediate | 786 | 1.70% | 0.00% | 5.98% | 92.37% | NA |
| Temperate Japonica | 767 | 53.50% | 0.00% | 2.09% | 44.46% | NA |
| Tropical Japonica | 504 | 8.90% | 0.00% | 2.38% | 88.69% | NA |
| Japonica Intermediate | 241 | 54.40% | 0.00% | 1.24% | 44.40% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 30.21% | 69.79% | NA |
| Intermediate | 90 | 16.70% | 0.00% | 14.44% | 68.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1007671811 | C -> A | LOC_Os10g14130.1 | missense_variant ; p.Val144Phe; MODERATE | nonsynonymous_codon ; V144F | Average:6.753; most accessible tissue: Minghui63 panicle, score: 16.27 | benign  |
0.289 |
DELETERIOUS | 0.02 |
| vg1007671811 | C -> DEL | LOC_Os10g14130.1 | N | frameshift_variant | Average:6.753; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |