Search for Variation information by Variation ID:
Detailed information for vg0800164390:
| Variant ID: vg0800164390 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 164390 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ATTCCAGGCTTCATCGTAACCATTGCAAGGAAGTCATTGTATGAAGAAGGGCAGACGTGTAGCATGCTAAACTGACACGTGGTGGACAAGAATGACCGGT[C/T]
TGTGACTGGTCTGACGCCGGTCGCGTCATCGGCAGACAACCGTGCTCCCACGATGCATCTGCCTCCGGTGGAGTGGAGGTAGGTATGACCCATCTCGTCG
Reverse complement sequence
CGACGAGATGGGTCATACCTACCTCCACTCCACCGGAGGCAGATGCATCGTGGGAGCACGGTTGTCTGCCGATGACGCGACCGGCGTCAGACCAGTCACA[G/A]
ACCGGTCATTCTTGTCCACCACGTGTCAGTTTAGCATGCTACACGTCTGCCCTTCTTCATACAATGACTTCCTTGCAATGGTTACGATGAAGCCTGGAAT
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 | 70.50% | 1.50% | 8.19% | 19.89% | NA |
| All Indica | 2759 | 62.20% | 2.50% | 12.00% | 23.27% | NA |
| All Japonica | 1512 | 89.00% | 0.00% | 0.46% | 10.52% | NA |
| Aus | 269 | 66.50% | 0.00% | 14.50% | 18.96% | NA |
| Indica I | 595 | 58.20% | 1.30% | 14.12% | 26.39% | NA |
| Indica II | 465 | 68.60% | 2.20% | 11.83% | 17.42% | NA |
| Indica III | 913 | 62.00% | 3.40% | 9.20% | 25.41% | NA |
| Indica Intermediate | 786 | 61.80% | 2.50% | 13.74% | 21.88% | NA |
| Temperate Japonica | 767 | 97.70% | 0.00% | 0.26% | 2.09% | NA |
| Tropical Japonica | 504 | 76.00% | 0.00% | 0.60% | 23.41% | NA |
| Japonica Intermediate | 241 | 88.80% | 0.00% | 0.83% | 10.37% | NA |
| VI/Aromatic | 96 | 30.20% | 0.00% | 3.12% | 66.67% | NA |
| Intermediate | 90 | 65.60% | 0.00% | 7.78% | 26.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0800164390 | C -> T | LOC_Os08g01250.1 | missense_variant ; p.Asp32Asn; MODERATE | nonsynonymous_codon ; D32N | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
0.614 |
TOLERATED | 0.54 |
| vg0800164390 | C -> DEL | LOC_Os08g01250.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |