Search for Variation information by Variation ID:
Detailed information for vg1201715563:
| Variant ID: vg1201715563 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 1715563 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TCGCCCATGCTAGGACGACGTCGCCGCGCCGCCGACGGGGATGCCCCGATGCAAGATGTCGCGAGATGTCCTCCTGGGCCTCGCGCTGACGAAGGCGTGC[G/C]
ACGCGAGGCAGGAGGAGTGCGCCGTGTGCCTCAGGGACTTCGAGGAGAAAGACATGCTGAGGACGATGCCGTGTAACCACTCCTTCCACGAGATCTGCCT
Reverse complement sequence
AGGCAGATCTCGTGGAAGGAGTGGTTACACGGCATCGTCCTCAGCATGTCTTTCTCCTCGAAGTCCCTGAGGCACACGGCGCACTCCTCCTGCCTCGCGT[C/G]
GCACGCCTTCGTCAGCGCGAGGCCCAGGAGGACATCTCGCGACATCTTGCATCGGGGCATCCCCGTCGGCGGCGCGGCGACGTCGTCCTAGCATGGGCGA
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 44.40% | 0.10% | 1.69% | 53.83% | NA |
| All Indica | 2759 | 9.10% | 0.10% | 2.68% | 88.11% | NA |
| All Japonica | 1512 | 97.20% | 0.10% | 0.07% | 2.65% | NA |
| Aus | 269 | 82.90% | 0.00% | 1.49% | 15.61% | NA |
| Indica I | 595 | 3.70% | 0.00% | 2.69% | 93.61% | NA |
| Indica II | 465 | 4.70% | 0.20% | 2.15% | 92.90% | NA |
| Indica III | 913 | 11.00% | 0.10% | 2.63% | 86.31% | NA |
| Indica Intermediate | 786 | 13.70% | 0.00% | 3.05% | 83.21% | NA |
| Temperate Japonica | 767 | 95.70% | 0.00% | 0.13% | 4.17% | NA |
| Tropical Japonica | 504 | 98.80% | 0.00% | 0.00% | 1.19% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.40% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 94.80% | 2.10% | 0.00% | 3.12% | NA |
| Intermediate | 90 | 67.80% | 0.00% | 1.11% | 31.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1201715563 | G -> C | LOC_Os12g04090.1 | missense_variant ; p.Asp130His; MODERATE | nonsynonymous_codon ; D130H | Average:63.904; most accessible tissue: Callus, score: 91.31 | probably damaging  |
2.561 |
DELETERIOUS | 0.01 |
| vg1201715563 | G -> DEL | LOC_Os12g04090.1 | N | frameshift_variant | Average:63.904; most accessible tissue: Callus, score: 91.31 | N | N | N | N |