Search for Variation information by Variation ID:
Detailed information for vg1012224147:
| Variant ID: vg1012224147 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 12224147 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ACGCTGGCCGGTACGAGGCTTGCTGCGGCCGCTGGTCGCTGGGTCTCGCCGGTATACCTACATATCCATGATCCTGGGTCTCGCAATGCACGGCCGCGGC[G/A]
AGGATGCCCTGTCTCTATTCGCCAGCATGCAACGAGCCGGCGTGACGCCGAACGAGGTGACCCTCCTCGGCGTCCTCACGGCGTGCTGTCATGCCGGACT
Reverse complement sequence
AGTCCGGCATGACAGCACGCCGTGAGGACGCCGAGGAGGGTCACCTCGTTCGGCGTCACGCCGGCTCGTTGCATGCTGGCGAATAGAGACAGGGCATCCT[C/T]
GCCGCGGCCGTGCATTGCGAGACCCAGGATCATGGATATGTAGGTATACCGGCGAGACCCAGCGACCAGCGGCCGCAGCAAGCCTCGTACCGGCCAGCGT
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 | 48.70% | 0.20% | 1.61% | 49.53% | NA |
| All Indica | 2759 | 31.40% | 0.20% | 2.50% | 65.93% | NA |
| All Japonica | 1512 | 88.40% | 0.10% | 0.07% | 11.38% | NA |
| Aus | 269 | 13.00% | 0.00% | 1.49% | 85.50% | NA |
| Indica I | 595 | 10.60% | 0.50% | 3.87% | 85.04% | NA |
| Indica II | 465 | 39.80% | 0.00% | 3.01% | 57.20% | NA |
| Indica III | 913 | 35.30% | 0.20% | 2.19% | 62.32% | NA |
| Indica Intermediate | 786 | 37.50% | 0.10% | 1.53% | 60.81% | NA |
| Temperate Japonica | 767 | 95.60% | 0.00% | 0.00% | 4.43% | NA |
| Tropical Japonica | 504 | 81.90% | 0.00% | 0.00% | 18.06% | NA |
| Japonica Intermediate | 241 | 79.30% | 0.80% | 0.41% | 19.50% | NA |
| VI/Aromatic | 96 | 9.40% | 0.00% | 0.00% | 90.62% | NA |
| Intermediate | 90 | 61.10% | 0.00% | 2.22% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1012224147 | G -> A | LOC_Os10g23830.1 | missense_variant ; p.Glu81Lys; MODERATE | nonsynonymous_codon ; E81K | Average:12.993; most accessible tissue: Callus, score: 37.216 | benign  |
1.361 |
TOLERATED | 0.06 |
| vg1012224147 | G -> DEL | LOC_Os10g23830.1 | N | frameshift_variant | Average:12.993; most accessible tissue: Callus, score: 37.216 | N | N | N | N |