Search for Variation information by Variation ID:
Detailed information for vg0800164360:
| Variant ID: vg0800164360 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 164360 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AGAGTTGGCACGTCAGCCCCGGCCAGATACATTCCAGGCTTCATCGTAACCATTGCAAGGAAGTCATTGTATGAAGAAGGGCAGACGTGTAGCATGCTAA[A/G]
CTGACACGTGGTGGACAAGAATGACCGGTCTGTGACTGGTCTGACGCCGGTCGCGTCATCGGCAGACAACCGTGCTCCCACGATGCATCTGCCTCCGGTG
Reverse complement sequence
CACCGGAGGCAGATGCATCGTGGGAGCACGGTTGTCTGCCGATGACGCGACCGGCGTCAGACCAGTCACAGACCGGTCATTCTTGTCCACCACGTGTCAG[T/C]
TTAGCATGCTACACGTCTGCCCTTCTTCATACAATGACTTCCTTGCAATGGTTACGATGAAGCCTGGAATGTATCTGGCCGGGGCTGACGTGCCAACTCT
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 | 74.40% | 1.20% | 6.01% | 18.39% | NA |
| All Indica | 2759 | 72.90% | 0.40% | 5.40% | 21.31% | NA |
| All Japonica | 1512 | 88.90% | 0.30% | 0.79% | 10.05% | NA |
| Aus | 269 | 27.90% | 14.50% | 40.15% | 17.47% | NA |
| Indica I | 595 | 67.20% | 0.20% | 8.74% | 23.87% | NA |
| Indica II | 465 | 78.90% | 0.20% | 5.16% | 15.70% | NA |
| Indica III | 913 | 72.70% | 0.50% | 2.30% | 24.42% | NA |
| Indica Intermediate | 786 | 73.80% | 0.50% | 6.62% | 19.08% | NA |
| Temperate Japonica | 767 | 98.00% | 0.00% | 0.13% | 1.83% | NA |
| Tropical Japonica | 504 | 74.80% | 0.80% | 1.79% | 22.62% | NA |
| Japonica Intermediate | 241 | 89.20% | 0.00% | 0.83% | 9.96% | NA |
| VI/Aromatic | 96 | 30.20% | 1.00% | 5.21% | 63.54% | NA |
| Intermediate | 90 | 65.60% | 0.00% | 11.11% | 23.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0800164360 | A -> G | LOC_Os08g01250.1 | missense_variant ; p.Phe42Leu; MODERATE | nonsynonymous_codon ; F42L | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
0.641 |
TOLERATED | 0.11 |
| vg0800164360 | A -> DEL | LOC_Os08g01250.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |