Search for Variation information by Variation ID:
Detailed information for vg0800164366:
| Variant ID: vg0800164366 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 164366 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GGCACGTCAGCCCCGGCCAGATACATTCCAGGCTTCATCGTAACCATTGCAAGGAAGTCATTGTATGAAGAAGGGCAGACGTGTAGCATGCTAAACTGAC[A/G]
CGTGGTGGACAAGAATGACCGGTCTGTGACTGGTCTGACGCCGGTCGCGTCATCGGCAGACAACCGTGCTCCCACGATGCATCTGCCTCCGGTGGAGTGG
Reverse complement sequence
CCACTCCACCGGAGGCAGATGCATCGTGGGAGCACGGTTGTCTGCCGATGACGCGACCGGCGTCAGACCAGTCACAGACCGGTCATTCTTGTCCACCACG[T/C]
GTCAGTTTAGCATGCTACACGTCTGCCCTTCTTCATACAATGACTTCCTTGCAATGGTTACGATGAAGCCTGGAATGTATCTGGCCGGGGCTGACGTGCC
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 76.20% | 0.20% | 4.15% | 19.53% | NA |
| All Indica | 2759 | 71.30% | 0.30% | 5.73% | 22.69% | NA |
| All Japonica | 1512 | 89.30% | 0.00% | 0.26% | 10.45% | NA |
| Aus | 269 | 69.90% | 0.00% | 11.15% | 18.96% | NA |
| Indica I | 595 | 66.20% | 0.20% | 8.24% | 25.38% | NA |
| Indica II | 465 | 78.30% | 0.20% | 4.52% | 16.99% | NA |
| Indica III | 913 | 72.00% | 0.50% | 2.30% | 25.19% | NA |
| Indica Intermediate | 786 | 70.20% | 0.10% | 8.52% | 21.12% | NA |
| Temperate Japonica | 767 | 97.90% | 0.00% | 0.13% | 1.96% | NA |
| Tropical Japonica | 504 | 76.40% | 0.00% | 0.20% | 23.41% | NA |
| Japonica Intermediate | 241 | 88.80% | 0.00% | 0.83% | 10.37% | NA |
| VI/Aromatic | 96 | 32.30% | 0.00% | 1.04% | 66.67% | NA |
| Intermediate | 90 | 70.00% | 0.00% | 3.33% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0800164366 | A -> G | LOC_Os08g01250.1 | missense_variant ; p.Cys40Arg; MODERATE | nonsynonymous_codon ; C40R | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
-0.061 |
TOLERATED | 0.66 |
| vg0800164366 | A -> DEL | LOC_Os08g01250.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |