Search for Variation information by Variation ID:
Detailed information for vg1114173460:
| Variant ID: vg1114173460 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 14173460 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 363. )
Flanking Sequence (100 bp) in Reference Genome:
CTCATGACTGTCACGTGTTGATGACACAACTGCTACCAGTTGTAATAAGGGGTATCCTTCCAGACAATGTCCGGACAACAATAACAAAGCTATGTGCATT[C/A]
ATGAACGCAATTTCGCAGAAGGTCATCGATCCGGATAGATTAGAAGCCCTTCAGAATGAAGTGGTGCAATGTCTCGTCAGTTTTGAGTTGATATTTCCAC
Reverse complement sequence
GTGGAAATATCAACTCAAAACTGACGAGACATTGCACCACTTCATTCTGAAGGGCTTCTAATCTATCCGGATCGATGACCTTCTGCGAAATTGCGTTCAT[G/T]
AATGCACATAGCTTTGTTATTGTTGTCCGGACATTGTCTGGAAGGATACCCCTTATTACAACTGGTAGCAGTTGTGTCATCAACACGTGACAGTCATGAG
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 | 8.00% | 0.10% | 6.71% | 85.15% | NA |
| All Indica | 2759 | 8.90% | 0.30% | 5.15% | 85.68% | NA |
| All Japonica | 1512 | 3.10% | 0.00% | 9.66% | 87.24% | NA |
| Aus | 269 | 21.90% | 0.00% | 4.09% | 73.98% | NA |
| Indica I | 595 | 4.20% | 0.50% | 5.38% | 89.92% | NA |
| Indica II | 465 | 12.70% | 0.00% | 5.38% | 81.94% | NA |
| Indica III | 913 | 9.60% | 0.20% | 5.26% | 84.88% | NA |
| Indica Intermediate | 786 | 9.40% | 0.30% | 4.71% | 85.62% | NA |
| Temperate Japonica | 767 | 1.20% | 0.00% | 7.82% | 91.00% | NA |
| Tropical Japonica | 504 | 6.70% | 0.00% | 11.90% | 81.35% | NA |
| Japonica Intermediate | 241 | 1.70% | 0.00% | 10.79% | 87.55% | NA |
| VI/Aromatic | 96 | 20.80% | 0.00% | 16.67% | 62.50% | NA |
| Intermediate | 90 | 6.70% | 0.00% | 2.22% | 91.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1114173460 | C -> A | LOC_Os11g24860.1 | missense_variant ; p.Phe697Leu; MODERATE | nonsynonymous_codon ; F697L | Average:7.227; most accessible tissue: Zhenshan97 root, score: 12.891 | benign  |
0.9 |
DELETERIOUS | 0.00 |
| vg1114173460 | C -> DEL | LOC_Os11g24860.1 | N | frameshift_variant | Average:7.227; most accessible tissue: Zhenshan97 root, score: 12.891 | N | N | N | N |