Search for Variation information by Variation ID:
Detailed information for vg0620602984:
| Variant ID: vg0620602984 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 20602984 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TTACCCGAATATGTGCTACTGCAACATTTCCATATAGGTTTGGATAAGGAGTCTGCATTCTATCTGGACATAACCGTCGGAGGATCGTTGATGCACAAAA[C/T]
GCCGTCGGAAGGAAGAACAATTTTGGATCATATTCTAGAAAATACTTCCTTCATGACGCAATCTGATGAACCCCAACCGGAGGCATACGTGTCCAAAATA
Reverse complement sequence
TATTTTGGACACGTATGCCTCCGGTTGGGGTTCATCAGATTGCGTCATGAAGGAAGTATTTTCTAGAATATGATCCAAAATTGTTCTTCCTTCCGACGGC[G/A]
TTTTGTGCATCAACGATCCTCCGACGGTTATGTCCAGATAGAATGCAGACTCCTTATCCAAACCTATATGGAAATGTTGCAGTAGCACATATTCGGGTAA
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.60% | 1.30% | 0.02% | 1.12% | NA |
| All Indica | 2759 | 99.90% | 0.10% | 0.00% | 0.07% | NA |
| All Japonica | 1512 | 96.60% | 0.20% | 0.00% | 3.24% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.80% | 0.10% | 0.00% | 0.11% | NA |
| Indica Intermediate | 786 | 99.70% | 0.10% | 0.00% | 0.13% | NA |
| Temperate Japonica | 767 | 99.20% | 0.00% | 0.00% | 0.78% | NA |
| Tropical Japonica | 504 | 99.00% | 0.00% | 0.00% | 0.99% | NA |
| Japonica Intermediate | 241 | 83.00% | 1.20% | 0.00% | 15.77% | NA |
| VI/Aromatic | 96 | 47.90% | 52.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 90.00% | 6.70% | 1.11% | 2.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0620602984 | C -> T | LOC_Os06g35340.1 | missense_variant ; p.Thr143Met; MODERATE | nonsynonymous_codon ; T143M | Average:12.346; most accessible tissue: Zhenshan97 root, score: 16.934 | benign  |
0.988 |
DELETERIOUS | 0.04 |
| vg0620602984 | C -> DEL | LOC_Os06g35340.1 | N | frameshift_variant | Average:12.346; most accessible tissue: Zhenshan97 root, score: 16.934 | N | N | N | N |