Search for Variation information by Variation ID:
Detailed information for vg0625222953:
| Variant ID: vg0625222953 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 25222953 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GTCCGTGACAGCGGCAACGTGCGGCTCTGGGGCGTCTGGAGTGAAGGTCACACGCGCACGAGTGCGAGGAAGGTACCAGCGAAGGTCACACTTGCTGCAG[C/T]
GTAAAGTCCTCCCACCTGCTTCTGACTCATCCATATCATTTCTGATGCGTCTAGTTTGGCGTCGACCCTTTTTCACCCTAAACTTAGATGGATCTGGAAT
Reverse complement sequence
ATTCCAGATCCATCTAAGTTTAGGGTGAAAAAGGGTCGACGCCAAACTAGACGCATCAGAAATGATATGGATGAGTCAGAAGCAGGTGGGAGGACTTTAC[G/A]
CTGCAGCAAGTGTGACCTTCGCTGGTACCTTCCTCGCACTCGTGCGCGTGTGACCTTCACTCCAGACGCCCCAGAGCCGCACGTTGCCGCTGTCACGGAC
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 | 16.40% | 0.10% | 14.52% | 68.92% | NA |
| All Indica | 2759 | 1.70% | 0.00% | 12.47% | 85.83% | NA |
| All Japonica | 1512 | 46.10% | 0.40% | 13.16% | 40.34% | NA |
| Aus | 269 | 3.00% | 0.00% | 32.34% | 64.68% | NA |
| Indica I | 595 | 1.50% | 0.00% | 10.92% | 87.56% | NA |
| Indica II | 465 | 3.40% | 0.00% | 11.18% | 85.38% | NA |
| Indica III | 913 | 0.80% | 0.00% | 11.39% | 87.84% | NA |
| Indica Intermediate | 786 | 1.90% | 0.00% | 15.65% | 82.44% | NA |
| Temperate Japonica | 767 | 72.80% | 0.30% | 3.91% | 23.08% | NA |
| Tropical Japonica | 504 | 8.50% | 0.20% | 25.79% | 65.48% | NA |
| Japonica Intermediate | 241 | 39.80% | 1.20% | 16.18% | 42.74% | NA |
| VI/Aromatic | 96 | 13.50% | 0.00% | 34.38% | 52.08% | NA |
| Intermediate | 90 | 13.30% | 0.00% | 25.56% | 61.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0625222953 | C -> T | LOC_Os06g42010.1 | missense_variant ; p.Arg732His; MODERATE | nonsynonymous_codon ; R732H | Average:4.969; most accessible tissue: Minghui63 panicle, score: 7.125 | probably damaging  |
2.235 |
DELETERIOUS | 0.04 |
| vg0625222953 | C -> DEL | LOC_Os06g42010.1 | N | frameshift_variant | Average:4.969; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |