Search for Variation information by Variation ID:
Detailed information for vg1012224168:
| Variant ID: vg1012224168 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 12224168 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GCTGCGGCCGCTGGTCGCTGGGTCTCGCCGGTATACCTACATATCCATGATCCTGGGTCTCGCAATGCACGGCCGCGGCGAGGATGCCCTGTCTCTATTC[G/A]
CCAGCATGCAACGAGCCGGCGTGACGCCGAACGAGGTGACCCTCCTCGGCGTCCTCACGGCGTGCTGTCATGCCGGACTCATCGAGGAGGGGCTCCAGCA
Reverse complement sequence
TGCTGGAGCCCCTCCTCGATGAGTCCGGCATGACAGCACGCCGTGAGGACGCCGAGGAGGGTCACCTCGTTCGGCGTCACGCCGGCTCGTTGCATGCTGG[C/T]
GAATAGAGACAGGGCATCCTCGCCGCGGCCGTGCATTGCGAGACCCAGGATCATGGATATGTAGGTATACCGGCGAGACCCAGCGACCAGCGGCCGCAGC
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 | 49.00% | 0.20% | 1.80% | 48.94% | NA |
| All Indica | 2759 | 31.70% | 0.00% | 2.68% | 65.60% | NA |
| All Japonica | 1512 | 89.20% | 0.70% | 0.07% | 10.12% | NA |
| Aus | 269 | 11.20% | 0.00% | 2.60% | 86.25% | NA |
| Indica I | 595 | 11.60% | 0.00% | 3.87% | 84.54% | NA |
| Indica II | 465 | 39.40% | 0.00% | 3.66% | 56.99% | NA |
| Indica III | 913 | 35.60% | 0.00% | 2.19% | 62.21% | NA |
| Indica Intermediate | 786 | 37.90% | 0.00% | 1.78% | 60.31% | NA |
| Temperate Japonica | 767 | 97.40% | 0.00% | 0.00% | 2.61% | NA |
| Tropical Japonica | 504 | 80.20% | 2.00% | 0.20% | 17.66% | NA |
| Japonica Intermediate | 241 | 81.70% | 0.00% | 0.00% | 18.26% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1012224168 | G -> A | LOC_Os10g23830.1 | missense_variant ; p.Ala88Thr; MODERATE | nonsynonymous_codon ; A88T | Average:12.935; most accessible tissue: Callus, score: 37.216 | possibly damaging  |
1.571 |
TOLERATED | 0.69 |
| vg1012224168 | G -> DEL | LOC_Os10g23830.1 | N | frameshift_variant | Average:12.935; most accessible tissue: Callus, score: 37.216 | N | N | N | N |