Search for Variation information by Variation ID:
Detailed information for vg1012224142:
| Variant ID: vg1012224142 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 12224142 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GTTGAACGCTGGCCGGTACGAGGCTTGCTGCGGCCGCTGGTCGCTGGGTCTCGCCGGTATACCTACATATCCATGATCCTGGGTCTCGCAATGCACGGCC[G/A]
CGGCGAGGATGCCCTGTCTCTATTCGCCAGCATGCAACGAGCCGGCGTGACGCCGAACGAGGTGACCCTCCTCGGCGTCCTCACGGCGTGCTGTCATGCC
Reverse complement sequence
GGCATGACAGCACGCCGTGAGGACGCCGAGGAGGGTCACCTCGTTCGGCGTCACGCCGGCTCGTTGCATGCTGGCGAATAGAGACAGGGCATCCTCGCCG[C/T]
GGCCGTGCATTGCGAGACCCAGGATCATGGATATGTAGGTATACCGGCGAGACCCAGCGACCAGCGGCCGCAGCAAGCCTCGTACCGGCCAGCGTTCAAC
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 | 49.10% | 0.30% | 1.61% | 49.01% | NA |
| All Indica | 2759 | 31.20% | 0.40% | 2.57% | 65.78% | NA |
| All Japonica | 1512 | 89.80% | 0.00% | 0.00% | 10.19% | NA |
| Aus | 269 | 13.40% | 0.40% | 1.12% | 85.13% | NA |
| Indica I | 595 | 11.10% | 0.30% | 3.87% | 84.71% | NA |
| Indica II | 465 | 39.60% | 0.00% | 3.23% | 57.20% | NA |
| Indica III | 913 | 34.90% | 0.40% | 2.41% | 62.21% | NA |
| Indica Intermediate | 786 | 37.20% | 0.80% | 1.40% | 60.69% | NA |
| Temperate Japonica | 767 | 97.40% | 0.00% | 0.00% | 2.61% | NA |
| Tropical Japonica | 504 | 82.10% | 0.00% | 0.00% | 17.86% | NA |
| Japonica Intermediate | 241 | 81.70% | 0.00% | 0.00% | 18.26% | NA |
| VI/Aromatic | 96 | 10.40% | 0.00% | 1.04% | 88.54% | NA |
| Intermediate | 90 | 62.20% | 0.00% | 1.11% | 36.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1012224142 | G -> A | LOC_Os10g23830.1 | missense_variant ; p.Arg79His; MODERATE | nonsynonymous_codon ; R79H | Average:12.993; most accessible tissue: Callus, score: 37.216 | benign  |
0.427 |
TOLERATED | 0.11 |
| vg1012224142 | G -> DEL | LOC_Os10g23830.1 | N | frameshift_variant | Average:12.993; most accessible tissue: Callus, score: 37.216 | N | N | N | N |