Search for Variation information by Variation ID:
Detailed information for vg0800164338:
| Variant ID: vg0800164338 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 164338 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CGGAGCCGGCGTGGGAACTCCTAGAGTTGGCACGTCAGCCCCGGCCAGATACATTCCAGGCTTCATCGTAACCATTGCAAGGAAGTCATTGTATGAAGAA[G/A]
GGCAGACGTGTAGCATGCTAAACTGACACGTGGTGGACAAGAATGACCGGTCTGTGACTGGTCTGACGCCGGTCGCGTCATCGGCAGACAACCGTGCTCC
Reverse complement sequence
GGAGCACGGTTGTCTGCCGATGACGCGACCGGCGTCAGACCAGTCACAGACCGGTCATTCTTGTCCACCACGTGTCAGTTTAGCATGCTACACGTCTGCC[C/T]
TTCTTCATACAATGACTTCCTTGCAATGGTTACGATGAAGCCTGGAATGTATCTGGCCGGGGCTGACGTGCCAACTCTAGGAGTTCCCACGCCGGCTCCG
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 74.60% | 0.70% | 5.82% | 18.83% | NA |
| All Indica | 2759 | 73.10% | 0.10% | 4.82% | 21.89% | NA |
| All Japonica | 1512 | 88.90% | 0.10% | 0.79% | 10.25% | NA |
| Aus | 269 | 28.30% | 10.80% | 43.12% | 17.84% | NA |
| Indica I | 595 | 67.60% | 0.00% | 8.57% | 23.87% | NA |
| Indica II | 465 | 79.40% | 0.00% | 4.73% | 15.91% | NA |
| Indica III | 913 | 73.20% | 0.00% | 1.75% | 25.08% | NA |
| Indica Intermediate | 786 | 73.70% | 0.50% | 5.60% | 20.23% | NA |
| Temperate Japonica | 767 | 98.00% | 0.00% | 0.13% | 1.83% | NA |
| Tropical Japonica | 504 | 74.80% | 0.20% | 1.79% | 23.21% | NA |
| Japonica Intermediate | 241 | 89.20% | 0.00% | 0.83% | 9.96% | NA |
| VI/Aromatic | 96 | 31.20% | 0.00% | 6.25% | 62.50% | NA |
| Intermediate | 90 | 65.60% | 0.00% | 8.89% | 25.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0800164338 | G -> A | LOC_Os08g01250.1 | missense_variant ; p.Pro49Leu; MODERATE | nonsynonymous_codon ; P49L | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
0.617 |
DELETERIOUS | 0.01 |
| vg0800164338 | G -> DEL | LOC_Os08g01250.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |