Search for Variation information by Variation ID:
Detailed information for vg0800164332:
| Variant ID: vg0800164332 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 164332 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 80. )
Flanking Sequence (100 bp) in Reference Genome:
CCTAGCCGGAGCCGGCGTGGGAACTCCTAGAGTTGGCACGTCAGCCCCGGCCAGATACATTCCAGGCTTCATCGTAACCATTGCAAGGAAGTCATTGTAT[G/A]
AAGAAGGGCAGACGTGTAGCATGCTAAACTGACACGTGGTGGACAAGAATGACCGGTCTGTGACTGGTCTGACGCCGGTCGCGTCATCGGCAGACAACCG
Reverse complement sequence
CGGTTGTCTGCCGATGACGCGACCGGCGTCAGACCAGTCACAGACCGGTCATTCTTGTCCACCACGTGTCAGTTTAGCATGCTACACGTCTGCCCTTCTT[C/T]
ATACAATGACTTCCTTGCAATGGTTACGATGAAGCCTGGAATGTATCTGGCCGGGGCTGACGTGCCAACTCTAGGAGTTCCCACGCCGGCTCCGGCTAGG
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 | 38.50% | 26.30% | 16.61% | 18.58% | NA |
| All Indica | 2759 | 8.90% | 43.90% | 26.28% | 20.95% | NA |
| All Japonica | 1512 | 88.10% | 0.60% | 0.86% | 10.45% | NA |
| Aus | 269 | 66.90% | 3.70% | 8.92% | 20.45% | NA |
| Indica I | 595 | 13.30% | 30.90% | 37.65% | 18.15% | NA |
| Indica II | 465 | 4.30% | 50.50% | 29.25% | 15.91% | NA |
| Indica III | 913 | 8.00% | 49.00% | 18.07% | 24.97% | NA |
| Indica Intermediate | 786 | 9.30% | 43.90% | 25.45% | 21.37% | NA |
| Temperate Japonica | 767 | 97.30% | 0.50% | 0.39% | 1.83% | NA |
| Tropical Japonica | 504 | 74.00% | 0.80% | 1.39% | 23.81% | NA |
| Japonica Intermediate | 241 | 88.40% | 0.40% | 1.24% | 9.96% | NA |
| VI/Aromatic | 96 | 20.80% | 1.00% | 11.46% | 66.67% | NA |
| Intermediate | 90 | 48.90% | 12.20% | 13.33% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0800164332 | G -> A | LOC_Os08g01250.1 | missense_variant ; p.Ser51Leu; MODERATE | nonsynonymous_codon ; S51L | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | possibly damaging  |
1.869 |
DELETERIOUS | 0.01 |
| vg0800164332 | G -> DEL | LOC_Os08g01250.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |