Search for Variation information by Variation ID:
Detailed information for vg0410079767:
| Variant ID: vg0410079767 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 10079767 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CAGCAGTGTAGTAGGTGGCCGAATCGGATTCCAGCACTTGGAGGATTTGATCTTGATATCTTCTTGTTCATCCATGATGTGAGCAATGGTTGCATCTGTG[G/C]
TAGCCATGGTCACATCATCCTCCCCTTCTTCACGGAAAACCGTCCTCGGTCTTTTGGAATCATCGTCTTTTTCGCTTTGGAAGTTCGTGGATTCGAGGTC
Reverse complement sequence
GACCTCGAATCCACGAACTTCCAAAGCGAAAAAGACGATGATTCCAAAAGACCGAGGACGGTTTTCCGTGAAGAAGGGGAGGATGATGTGACCATGGCTA[C/G]
CACAGATGCAACCATTGCTCACATCATGGATGAACAAGAAGATATCAAGATCAAATCCTCCAAGTGCTGGAATCCGATTCGGCCACCTACTACACTGCTG
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 29.50% | 0.30% | 5.18% | 65.00% | NA |
| All Indica | 2759 | 4.30% | 0.50% | 4.39% | 90.76% | NA |
| All Japonica | 1512 | 77.50% | 0.00% | 6.55% | 15.94% | NA |
| Aus | 269 | 4.10% | 0.40% | 2.23% | 93.31% | NA |
| Indica I | 595 | 4.90% | 0.30% | 4.87% | 89.92% | NA |
| Indica II | 465 | 4.90% | 0.40% | 4.30% | 90.32% | NA |
| Indica III | 913 | 2.50% | 1.10% | 4.27% | 92.11% | NA |
| Indica Intermediate | 786 | 5.60% | 0.10% | 4.20% | 90.08% | NA |
| Temperate Japonica | 767 | 96.50% | 0.00% | 0.52% | 3.00% | NA |
| Tropical Japonica | 504 | 50.40% | 0.00% | 17.66% | 31.94% | NA |
| Japonica Intermediate | 241 | 73.90% | 0.00% | 2.49% | 23.65% | NA |
| VI/Aromatic | 96 | 52.10% | 0.00% | 14.58% | 33.33% | NA |
| Intermediate | 90 | 45.60% | 0.00% | 5.56% | 48.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0410079767 | G -> C | LOC_Os04g18230.1 | missense_variant ; p.Thr3Ser; MODERATE | nonsynonymous_codon ; T3S | Average:12.886; most accessible tissue: Minghui63 panicle, score: 42.799 | benign  |
0.864 |
DELETERIOUS | 0.00 |
| vg0410079767 | G -> DEL | LOC_Os04g18230.1 | N | frameshift_variant | Average:12.886; most accessible tissue: Minghui63 panicle, score: 42.799 | N | N | N | N |