Search for Variation information by Variation ID:
Detailed information for vg1114174182:
| Variant ID: vg1114174182 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 14174182 |
| Reference Allele: C | Alternative Allele: T,A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GGACCGTCTGGGTCGATCGCGACATTCCAGGGATATGAGATCAATGGGTACACATTCTACACGAGAGCCCAAGACATGAAGAGCACGAACCAAAACAGCG[C/T,A]
TGTTCGTGTCGATGTCATGGGACACGATGGAACAACTGTCACGTATTACGGTGCCATCGAGGACATATGGGAACTTGACTATGGTCCTCTCAAGGTTCCT
Reverse complement sequence
AGGAACCTTGAGAGGACCATAGTCAAGTTCCCATATGTCCTCGATGGCACCGTAATACGTGACAGTTGTTCCATCGTGTCCCATGACATCGACACGAACA[G/A,T]
CGCTGTTTTGGTTCGTGCTCTTCATGTCTTGGGCTCTCGTGTAGAATGTGTACCCATTGATCTCATATCCCTGGAATGTCGCGATCGACCCAGACGGTCC
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 | 35.60% | 0.10% | 4.08% | 60.16% | T: 0.02% |
| All Indica | 2759 | 3.70% | 0.00% | 6.27% | 90.00% | NA |
| All Japonica | 1512 | 96.20% | 0.40% | 0.46% | 2.91% | T: 0.07% |
| Aus | 269 | 1.90% | 0.00% | 3.35% | 94.80% | NA |
| Indica I | 595 | 3.90% | 0.00% | 4.03% | 92.10% | NA |
| Indica II | 465 | 2.60% | 0.00% | 6.67% | 90.75% | NA |
| Indica III | 913 | 2.50% | 0.00% | 6.68% | 90.80% | NA |
| Indica Intermediate | 786 | 5.70% | 0.00% | 7.25% | 87.02% | NA |
| Temperate Japonica | 767 | 96.50% | 0.00% | 0.26% | 3.26% | NA |
| Tropical Japonica | 504 | 95.40% | 0.80% | 0.79% | 2.78% | T: 0.20% |
| Japonica Intermediate | 241 | 96.70% | 0.80% | 0.41% | 2.07% | NA |
| VI/Aromatic | 96 | 87.50% | 0.00% | 1.04% | 11.46% | NA |
| Intermediate | 90 | 41.10% | 0.00% | 3.33% | 55.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1114174182 | C -> T | LOC_Os11g24860.1 | missense_variant ; p.Ala938Val; MODERATE | nonsynonymous_codon ; A938V | Average:5.813; most accessible tissue: Callus, score: 19.27 | benign  |
0.508 |
TOLERATED | 0.24 |
| vg1114174182 | C -> A | LOC_Os11g24860.1 | missense_variant ; p.Ala938Asp; MODERATE | nonsynonymous_codon ; A938D | Average:5.813; most accessible tissue: Callus, score: 19.27 | benign |
0.504 |
DELETERIOUS | 0.04 |
| vg1114174182 | C -> DEL | LOC_Os11g24860.1 | N | frameshift_variant | Average:5.813; most accessible tissue: Callus, score: 19.27 | N | N | N | N |