Search for Variation information by Variation ID:
Detailed information for vg1012224109:
| Variant ID: vg1012224109 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 12224109 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CGCGAGCAGGATGTGGCCGTGCGCGAGAAGGCTGTTGAACGCTGGCCGGTACGAGGCTTGCTGCGGCCGCTGGTCGCTGGGTCTCGCCGGTATACCTACA[T/C]
ATCCATGATCCTGGGTCTCGCAATGCACGGCCGCGGCGAGGATGCCCTGTCTCTATTCGCCAGCATGCAACGAGCCGGCGTGACGCCGAACGAGGTGACC
Reverse complement sequence
GGTCACCTCGTTCGGCGTCACGCCGGCTCGTTGCATGCTGGCGAATAGAGACAGGGCATCCTCGCCGCGGCCGTGCATTGCGAGACCCAGGATCATGGAT[A/G]
TGTAGGTATACCGGCGAGACCCAGCGACCAGCGGCCGCAGCAAGCCTCGTACCGGCCAGCGTTCAACAGCCTTCTCGCGCACGGCCACATCCTGCTCGCG
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 48.30% | 0.40% | 1.46% | 49.85% | NA |
| All Indica | 2759 | 31.10% | 0.30% | 2.25% | 66.40% | NA |
| All Japonica | 1512 | 88.40% | 0.20% | 0.13% | 11.31% | NA |
| Aus | 269 | 10.40% | 2.20% | 0.74% | 86.62% | NA |
| Indica I | 595 | 10.80% | 0.50% | 3.19% | 85.55% | NA |
| Indica II | 465 | 39.10% | 0.00% | 2.58% | 58.28% | NA |
| Indica III | 913 | 34.50% | 0.30% | 1.97% | 63.20% | NA |
| Indica Intermediate | 786 | 37.70% | 0.30% | 1.65% | 60.43% | NA |
| Temperate Japonica | 767 | 95.60% | 0.00% | 0.00% | 4.43% | NA |
| Tropical Japonica | 504 | 81.70% | 0.00% | 0.00% | 18.25% | NA |
| Japonica Intermediate | 241 | 79.30% | 1.20% | 0.83% | 18.67% | NA |
| VI/Aromatic | 96 | 8.30% | 0.00% | 2.08% | 89.58% | NA |
| Intermediate | 90 | 58.90% | 2.20% | 1.11% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1012224109 | T -> C | LOC_Os10g23830.1 | missense_variant ; p.Ile68Thr; MODERATE | nonsynonymous_codon ; I68T | Average:12.993; most accessible tissue: Callus, score: 37.216 | benign  |
-1.489 |
TOLERATED | 1.00 |
| vg1012224109 | T -> DEL | LOC_Os10g23830.1 | N | frameshift_variant | Average:12.993; most accessible tissue: Callus, score: 37.216 | N | N | N | N |