Search for Variation information by Variation ID:
Detailed information for vg1012224171:
| Variant ID: vg1012224171 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 12224171 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GCGGCCGCTGGTCGCTGGGTCTCGCCGGTATACCTACATATCCATGATCCTGGGTCTCGCAATGCACGGCCGCGGCGAGGATGCCCTGTCTCTATTCGCC[A/G]
GCATGCAACGAGCCGGCGTGACGCCGAACGAGGTGACCCTCCTCGGCGTCCTCACGGCGTGCTGTCATGCCGGACTCATCGAGGAGGGGCTCCAGCAACT
Reverse complement sequence
AGTTGCTGGAGCCCCTCCTCGATGAGTCCGGCATGACAGCACGCCGTGAGGACGCCGAGGAGGGTCACCTCGTTCGGCGTCACGCCGGCTCGTTGCATGC[T/C]
GGCGAATAGAGACAGGGCATCCTCGCCGCGGCCGTGCATTGCGAGACCCAGGATCATGGATATGTAGGTATACCGGCGAGACCCAGCGACCAGCGGCCGC
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 48.70% | 0.10% | 1.97% | 49.28% | NA |
| All Indica | 2759 | 31.50% | 0.10% | 3.04% | 65.42% | NA |
| All Japonica | 1512 | 88.50% | 0.10% | 0.26% | 11.18% | NA |
| Aus | 269 | 10.80% | 0.40% | 1.86% | 86.99% | NA |
| Indica I | 595 | 10.90% | 0.00% | 4.87% | 84.20% | NA |
| Indica II | 465 | 39.40% | 0.00% | 3.87% | 56.77% | NA |
| Indica III | 913 | 35.40% | 0.20% | 2.30% | 62.10% | NA |
| Indica Intermediate | 786 | 37.80% | 0.00% | 2.04% | 60.18% | NA |
| Temperate Japonica | 767 | 95.60% | 0.00% | 0.00% | 4.43% | NA |
| Tropical Japonica | 504 | 81.90% | 0.00% | 0.20% | 17.86% | NA |
| Japonica Intermediate | 241 | 79.70% | 0.40% | 1.24% | 18.67% | NA |
| VI/Aromatic | 96 | 9.40% | 0.00% | 0.00% | 90.62% | NA |
| Intermediate | 90 | 62.20% | 0.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1012224171 | A -> G | LOC_Os10g23830.1 | missense_variant ; p.Ser89Gly; MODERATE | nonsynonymous_codon ; S89G | Average:12.876; most accessible tissue: Callus, score: 37.216 | benign  |
0.117 |
TOLERATED | 0.43 |
| vg1012224171 | A -> DEL | LOC_Os10g23830.1 | N | frameshift_variant | Average:12.876; most accessible tissue: Callus, score: 37.216 | N | N | N | N |