Search for Variation information by Variation ID:
Detailed information for vg1012224216:
| Variant ID: vg1012224216 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 12224216 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GATCCTGGGTCTCGCAATGCACGGCCGCGGCGAGGATGCCCTGTCTCTATTCGCCAGCATGCAACGAGCCGGCGTGACGCCGAACGAGGTGACCCTCCTC[G/A]
GCGTCCTCACGGCGTGCTGTCATGCCGGACTCATCGAGGAGGGGCTCCAGCAACTCGACGCCATGAGGAGGAACGAGATCGACAAGGTCCCCGGCTGCAG
Reverse complement sequence
CTGCAGCCGGGGACCTTGTCGATCTCGTTCCTCCTCATGGCGTCGAGTTGCTGGAGCCCCTCCTCGATGAGTCCGGCATGACAGCACGCCGTGAGGACGC[C/T]
GAGGAGGGTCACCTCGTTCGGCGTCACGCCGGCTCGTTGCATGCTGGCGAATAGAGACAGGGCATCCTCGCCGCGGCCGTGCATTGCGAGACCCAGGATC
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 | 49.30% | 0.00% | 2.14% | 48.56% | NA |
| All Indica | 2759 | 32.30% | 0.00% | 3.19% | 64.48% | NA |
| All Japonica | 1512 | 88.70% | 0.10% | 0.07% | 11.18% | NA |
| Aus | 269 | 11.50% | 0.00% | 3.35% | 85.13% | NA |
| Indica I | 595 | 12.80% | 0.00% | 4.71% | 82.52% | NA |
| Indica II | 465 | 40.00% | 0.00% | 4.52% | 55.48% | NA |
| Indica III | 913 | 35.50% | 0.10% | 2.74% | 61.66% | NA |
| Indica Intermediate | 786 | 38.80% | 0.00% | 1.78% | 59.41% | NA |
| Temperate Japonica | 767 | 95.70% | 0.00% | 0.00% | 4.30% | NA |
| Tropical Japonica | 504 | 81.70% | 0.00% | 0.20% | 18.06% | NA |
| Japonica Intermediate | 241 | 80.90% | 0.40% | 0.00% | 18.67% | NA |
| VI/Aromatic | 96 | 9.40% | 0.00% | 2.08% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1012224216 | G -> A | LOC_Os10g23830.1 | missense_variant ; p.Gly104Ser; MODERATE | nonsynonymous_codon ; G104S | Average:14.255; most accessible tissue: Callus, score: 56.934 | benign  |
0.937 |
TOLERATED | 0.34 |
| vg1012224216 | G -> DEL | LOC_Os10g23830.1 | N | frameshift_variant | Average:14.255; most accessible tissue: Callus, score: 56.934 | N | N | N | N |