Search for Variation information by Variation ID:
Detailed information for vg0800164423:
| Variant ID: vg0800164423 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 164423 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TCATTGTATGAAGAAGGGCAGACGTGTAGCATGCTAAACTGACACGTGGTGGACAAGAATGACCGGTCTGTGACTGGTCTGACGCCGGTCGCGTCATCGG[C/T]
AGACAACCGTGCTCCCACGATGCATCTGCCTCCGGTGGAGTGGAGGTAGGTATGACCCATCTCGTCGGATGGTCATTTGGATAGCAGCCATGGCAAATCT
Reverse complement sequence
AGATTTGCCATGGCTGCTATCCAAATGACCATCCGACGAGATGGGTCATACCTACCTCCACTCCACCGGAGGCAGATGCATCGTGGGAGCACGGTTGTCT[G/A]
CCGATGACGCGACCGGCGTCAGACCAGTCACAGACCGGTCATTCTTGTCCACCACGTGTCAGTTTAGCATGCTACACGTCTGCCCTTCTTCATACAATGA
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 38.40% | 0.70% | 9.44% | 51.54% | NA |
| All Indica | 2759 | 14.50% | 0.10% | 11.42% | 74.01% | NA |
| All Japonica | 1512 | 85.50% | 1.80% | 1.32% | 11.38% | NA |
| Aus | 269 | 21.20% | 0.00% | 36.43% | 42.38% | NA |
| Indica I | 595 | 21.30% | 0.00% | 6.22% | 72.44% | NA |
| Indica II | 465 | 16.10% | 0.00% | 10.32% | 73.55% | NA |
| Indica III | 913 | 9.10% | 0.00% | 15.12% | 75.79% | NA |
| Indica Intermediate | 786 | 14.50% | 0.40% | 11.70% | 73.41% | NA |
| Temperate Japonica | 767 | 93.70% | 3.50% | 0.13% | 2.61% | NA |
| Tropical Japonica | 504 | 71.60% | 0.00% | 3.77% | 24.60% | NA |
| Japonica Intermediate | 241 | 88.40% | 0.00% | 0.00% | 11.62% | NA |
| VI/Aromatic | 96 | 16.70% | 0.00% | 7.29% | 76.04% | NA |
| Intermediate | 90 | 53.30% | 1.10% | 6.67% | 38.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0800164423 | C -> T | LOC_Os08g01250.1 | missense_variant ; p.Ala21Thr; MODERATE | nonsynonymous_codon ; A21T | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | possibly damaging  |
1.571 |
DELETERIOUS | 0.02 |
| vg0800164423 | C -> DEL | LOC_Os08g01250.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |