Search for Variation information by Variation ID:
Detailed information for vg0206044763:
| Variant ID: vg0206044763 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 6044763 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GGTGTACGACACACCGGCGCTGTTGAACCGTGGGATTGACAGGAACCACCGCTCGTTCCTGTCAGCAGTCGAGGGTGCACAGCTCGGCACCTTCCGTCCA[C/T]
GCACGTCGCGCGAGTGGTTGCGTGTCGACCCCCGTCACATTCCTTGGTACGCGTATGTTCACATTTCAACTCAACTTTGCTTTGTGTTGTACTTATGTTT
Reverse complement sequence
AAACATAAGTACAACACAAAGCAAAGTTGAGTTGAAATGTGAACATACGCGTACCAAGGAATGTGACGGGGGTCGACACGCAACCACTCGCGCGACGTGC[G/A]
TGGACGGAAGGTGCCGAGCTGTGCACCCTCGACTGCTGACAGGAACGAGCGGTGGTTCCTGTCAATCCCACGGTTCAACAGCGCCGGTGTGTCGTACACC
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 35.90% | 0.60% | 25.20% | 38.34% | NA |
| All Indica | 2759 | 5.00% | 0.80% | 36.86% | 57.30% | NA |
| All Japonica | 1512 | 96.80% | 0.00% | 1.65% | 1.52% | NA |
| Aus | 269 | 5.60% | 2.20% | 46.84% | 45.35% | NA |
| Indica I | 595 | 2.20% | 0.30% | 35.46% | 62.02% | NA |
| Indica II | 465 | 5.20% | 2.60% | 36.77% | 55.48% | NA |
| Indica III | 913 | 6.80% | 0.00% | 39.32% | 53.89% | NA |
| Indica Intermediate | 786 | 5.10% | 1.00% | 35.11% | 58.78% | NA |
| Temperate Japonica | 767 | 97.90% | 0.00% | 1.04% | 1.04% | NA |
| Tropical Japonica | 504 | 96.20% | 0.00% | 1.98% | 1.79% | NA |
| Japonica Intermediate | 241 | 94.60% | 0.00% | 2.90% | 2.49% | NA |
| VI/Aromatic | 96 | 38.50% | 0.00% | 7.29% | 54.17% | NA |
| Intermediate | 90 | 44.40% | 0.00% | 17.78% | 37.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0206044763 | C -> T | LOC_Os02g11730.1 | missense_variant ; p.Arg907Cys; MODERATE | nonsynonymous_codon ; R907C | Average:16.669; most accessible tissue: Minghui63 panicle, score: 46.754 | probably damaging  |
2.729 |
DELETERIOUS | 0.00 |
| vg0206044763 | C -> DEL | LOC_Os02g11730.1 | N | frameshift_variant | Average:16.669; most accessible tissue: Minghui63 panicle, score: 46.754 | N | N | N | N |