Search for Variation information by Variation ID:
Detailed information for vg1101752685:
| Variant ID: vg1101752685 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 1752685 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.58, G: 0.42, others allele: 0.00, population size: 127. )
Flanking Sequence (100 bp) in Reference Genome:
CCAGTACACCTCTCCATGGTACACCACTCGATAGAACTCTTGTAGCATGTCGCGGATGCTCCGGGCATCGCTATTGGGGTCGATTCCTAGGCGTTGGAGC[G/A]
TGCGGTGGAATCTCACTGGAACTCGTGCTGCTGCCGCTGCCGGATCCATCCATCTCCCGGCGCTACGGACTATGGTGTGGATACTAGGGTCGACTCCCAA
Reverse complement sequence
TTGGGAGTCGACCCTAGTATCCACACCATAGTCCGTAGCGCCGGGAGATGGATGGATCCGGCAGCGGCAGCAGCACGAGTTCCAGTGAGATTCCACCGCA[C/T]
GCTCCAACGCCTAGGAATCGACCCCAATAGCGATGCCCGGAGCATCCGCGACATGCTACAAGAGTTCTATCGAGTGGTGTACCATGGAGAGGTGTACTGG
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 0.30% | 0.20% | 3.07% | 96.42% | NA |
| All Indica | 2759 | 0.40% | 0.00% | 0.72% | 98.80% | NA |
| All Japonica | 1512 | 0.00% | 0.50% | 3.37% | 96.16% | NA |
| Aus | 269 | 0.40% | 0.00% | 14.50% | 85.13% | NA |
| Indica I | 595 | 0.70% | 0.00% | 0.50% | 98.82% | NA |
| Indica II | 465 | 0.60% | 0.00% | 1.08% | 98.28% | NA |
| Indica III | 913 | 0.40% | 0.00% | 0.55% | 99.01% | NA |
| Indica Intermediate | 786 | 0.10% | 0.10% | 0.89% | 98.85% | NA |
| Temperate Japonica | 767 | 0.00% | 0.10% | 0.26% | 99.61% | NA |
| Tropical Japonica | 504 | 0.00% | 1.00% | 8.33% | 90.67% | NA |
| Japonica Intermediate | 241 | 0.00% | 0.40% | 2.90% | 96.68% | NA |
| VI/Aromatic | 96 | 2.10% | 0.00% | 36.46% | 61.46% | NA |
| Intermediate | 90 | 1.10% | 0.00% | 0.00% | 98.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1101752685 | G -> A | LOC_Os11g04280.1 | missense_variant ; p.Thr69Met; MODERATE | nonsynonymous_codon ; T69M | Average:7.736; most accessible tissue: Zhenshan97 flower, score: 15.748 | benign  |
0.399 |
DELETERIOUS | 0.00 |
| vg1101752685 | G -> DEL | LOC_Os11g04280.1 | N | frameshift_variant | Average:7.736; most accessible tissue: Zhenshan97 flower, score: 15.748 | N | N | N | N |