Search for Variation information by Variation ID:
Detailed information for vg0435226685:
| Variant ID: vg0435226685 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 35226685 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TCAGCGCCTCCGACCCAGGAAGATCTGCGTGGGGGGCCGGATGCCCGCATCGATATCGAGCGCCGGTGTAATGGCCGACGTGCTGCCCACGCAACGGAGG[G/A]
CGCCTCCTCGTCCGGAGTGTCACATCAACACGGACGCGGGGATCAGCCCTCCGTGCCCCCGGTTGGTGGTGTCGGCTGTAGAGCCTTTGTGGCGAGCCTT
Reverse complement sequence
AAGGCTCGCCACAAAGGCTCTACAGCCGACACCACCAACCGGGGGCACGGAGGGCTGATCCCCGCGTCCGTGTTGATGTGACACTCCGGACGAGGAGGCG[C/T]
CCTCCGTTGCGTGGGCAGCACGTCGGCCATTACACCGGCGCTCGATATCGATGCGGGCATCCGGCCCCCCACGCAGATCTTCCTGGGTCGGAGGCGCTGA
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 | 44.90% | 1.00% | 1.90% | 52.20% | NA |
| All Indica | 2759 | 10.70% | 0.00% | 2.14% | 87.13% | NA |
| All Japonica | 1512 | 94.20% | 3.00% | 1.92% | 0.86% | NA |
| Aus | 269 | 91.10% | 0.00% | 0.00% | 8.92% | NA |
| Indica I | 595 | 7.10% | 0.00% | 1.34% | 91.60% | NA |
| Indica II | 465 | 5.60% | 0.00% | 1.08% | 93.33% | NA |
| Indica III | 913 | 9.30% | 0.00% | 2.52% | 88.17% | NA |
| Indica Intermediate | 786 | 18.20% | 0.00% | 2.93% | 78.88% | NA |
| Temperate Japonica | 767 | 99.10% | 0.30% | 0.52% | 0.13% | NA |
| Tropical Japonica | 504 | 95.20% | 0.80% | 1.98% | 1.98% | NA |
| Japonica Intermediate | 241 | 76.30% | 16.60% | 6.22% | 0.83% | NA |
| VI/Aromatic | 96 | 88.50% | 0.00% | 1.04% | 10.42% | NA |
| Intermediate | 90 | 81.10% | 0.00% | 1.11% | 17.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0435226685 | G -> DEL | LOC_Os04g59220.1 | N | frameshift_variant | Average:9.639; most accessible tissue: Minghui63 panicle, score: 25.313 | N | N | N | N |
| vg0435226685 | G -> A | LOC_Os04g59220.1 | missense_variant ; p.Gly195Asp; MODERATE | nonsynonymous_codon ; G195D | Average:9.639; most accessible tissue: Minghui63 panicle, score: 25.313 | possibly damaging  |
1.911 |
DELETERIOUS | 0.01 |