Search for Variation information by Variation ID:
Detailed information for vg1105160507:
| Variant ID: vg1105160507 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5160507 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CCGGAACCTTGGGGGCCAACGGACGTTCCGAAGGCTCGCCACAAAGGCTCTACAGCCGACACCACCAACCGGGGGCACGAAGGGCTGATCCCCGCGTCCG[T/G]
GTTGATGTGACACTCCGGACGAGGAGGCGCCCTCCGTTGCGTGGGCAGCACGTCGACCATTACGCCGGCGCTCGATACTGATGCGGGCATCCGGCCCCCC
Reverse complement sequence
GGGGGGCCGGATGCCCGCATCAGTATCGAGCGCCGGCGTAATGGTCGACGTGCTGCCCACGCAACGGAGGGCGCCTCCTCGTCCGGAGTGTCACATCAAC[A/C]
CGGACGCGGGGATCAGCCCTTCGTGCCCCCGGTTGGTGGTGTCGGCTGTAGAGCCTTTGTGGCGAGCCTTCGGAACGTCCGTTGGCCCCCAAGGTTCCGG
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 13.20% | 0.20% | 24.99% | 61.68% | NA |
| All Indica | 2759 | 4.00% | 0.30% | 22.83% | 72.92% | NA |
| All Japonica | 1512 | 32.40% | 0.00% | 27.45% | 40.15% | NA |
| Aus | 269 | 0.70% | 0.00% | 28.25% | 71.00% | NA |
| Indica I | 595 | 3.40% | 0.00% | 4.20% | 92.44% | NA |
| Indica II | 465 | 1.10% | 1.10% | 18.28% | 79.57% | NA |
| Indica III | 913 | 2.00% | 0.00% | 40.96% | 57.06% | NA |
| Indica Intermediate | 786 | 8.40% | 0.40% | 18.58% | 72.65% | NA |
| Temperate Japonica | 767 | 36.80% | 0.00% | 16.43% | 46.81% | NA |
| Tropical Japonica | 504 | 17.70% | 0.00% | 45.63% | 36.71% | NA |
| Japonica Intermediate | 241 | 49.40% | 0.00% | 24.48% | 26.14% | NA |
| VI/Aromatic | 96 | 5.20% | 0.00% | 39.58% | 55.21% | NA |
| Intermediate | 90 | 17.80% | 0.00% | 24.44% | 57.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105160507 | T -> DEL | LOC_Os11g09660.1 | N | frameshift_variant | Average:9.342; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg1105160507 | T -> G | LOC_Os11g09660.1 | missense_variant ; p.His205Pro; MODERATE | nonsynonymous_codon ; H205P | Average:9.342; most accessible tissue: Zhenshan97 panicle, score: 16.188 | possibly damaging  |
1.674 |
DELETERIOUS | 0.00 |