Search for Variation information by Variation ID:
Detailed information for vg1012224195:
| Variant ID: vg1012224195 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 12224195 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CCGGTATACCTACATATCCATGATCCTGGGTCTCGCAATGCACGGCCGCGGCGAGGATGCCCTGTCTCTATTCGCCAGCATGCAACGAGCCGGCGTGACG[C/A]
CGAACGAGGTGACCCTCCTCGGCGTCCTCACGGCGTGCTGTCATGCCGGACTCATCGAGGAGGGGCTCCAGCAACTCGACGCCATGAGGAGGAACGAGAT
Reverse complement sequence
ATCTCGTTCCTCCTCATGGCGTCGAGTTGCTGGAGCCCCTCCTCGATGAGTCCGGCATGACAGCACGCCGTGAGGACGCCGAGGAGGGTCACCTCGTTCG[G/T]
CGTCACGCCGGCTCGTTGCATGCTGGCGAATAGAGACAGGGCATCCTCGCCGCGGCCGTGCATTGCGAGACCCAGGATCATGGATATGTAGGTATACCGG
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 49.10% | 0.20% | 1.76% | 48.96% | NA |
| All Indica | 2759 | 31.50% | 0.30% | 2.83% | 65.35% | NA |
| All Japonica | 1512 | 89.70% | 0.00% | 0.13% | 10.19% | NA |
| Aus | 269 | 11.20% | 0.00% | 1.12% | 87.73% | NA |
| Indica I | 595 | 11.90% | 0.00% | 3.70% | 84.37% | NA |
| Indica II | 465 | 40.40% | 0.00% | 3.23% | 56.34% | NA |
| Indica III | 913 | 34.50% | 0.90% | 2.52% | 62.10% | NA |
| Indica Intermediate | 786 | 37.70% | 0.00% | 2.29% | 60.05% | NA |
| Temperate Japonica | 767 | 97.30% | 0.00% | 0.13% | 2.61% | NA |
| Tropical Japonica | 504 | 81.90% | 0.00% | 0.20% | 17.86% | NA |
| Japonica Intermediate | 241 | 81.70% | 0.00% | 0.00% | 18.26% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1012224195 | C -> A | LOC_Os10g23830.1 | missense_variant ; p.Pro97Thr; MODERATE | nonsynonymous_codon ; P97T | Average:14.255; most accessible tissue: Callus, score: 56.934 | possibly damaging  |
1.891 |
TOLERATED | 0.09 |
| vg1012224195 | C -> DEL | LOC_Os10g23830.1 | N | frameshift_variant | Average:14.255; most accessible tissue: Callus, score: 56.934 | N | N | N | N |