Search for Variation information by Variation ID:
Detailed information for vg0620602925:
| Variant ID: vg0620602925 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 20602925 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TCAATCGGTGCAGCCTGTCCAGATTCACTAATTTAGTGCAGTCCGGACCAACCCTATCCTTACCCGAATATGTGCTACTGCAACATTTCCATATAGGTTT[G/C]
GATAAGGAGTCTGCATTCTATCTGGACATAACCGTCGGAGGATCGTTGATGCACAAAACGCCGTCGGAAGGAAGAACAATTTTGGATCATATTCTAGAAA
Reverse complement sequence
TTTCTAGAATATGATCCAAAATTGTTCTTCCTTCCGACGGCGTTTTGTGCATCAACGATCCTCCGACGGTTATGTCCAGATAGAATGCAGACTCCTTATC[C/G]
AAACCTATATGGAAATGTTGCAGTAGCACATATTCGGGTAAGGATAGGGTTGGTCCGGACTGCACTAAATTAGTGAATCTGGACAGGCTGCACCGATTGA
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 96.00% | 1.50% | 1.25% | 1.21% | NA |
| All Indica | 2759 | 99.80% | 0.00% | 0.11% | 0.07% | NA |
| All Japonica | 1512 | 88.40% | 4.50% | 3.64% | 3.51% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.17% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.00% | 0.00% | 0.11% | NA |
| Indica Intermediate | 786 | 99.60% | 0.00% | 0.25% | 0.13% | NA |
| Temperate Japonica | 767 | 87.50% | 5.00% | 6.78% | 0.78% | NA |
| Tropical Japonica | 504 | 98.60% | 0.00% | 0.20% | 1.19% | NA |
| Japonica Intermediate | 241 | 69.70% | 12.40% | 0.83% | 17.01% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 3.30% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0620602925 | G -> C | LOC_Os06g35340.1 | missense_variant ; p.Leu123Phe; MODERATE | nonsynonymous_codon ; L123F | Average:13.336; most accessible tissue: Minghui63 flag leaf, score: 17.373 | possibly damaging  |
1.952 |
DELETERIOUS | 0.00 |
| vg0620602925 | G -> DEL | LOC_Os06g35340.1 | N | frameshift_variant | Average:13.336; most accessible tissue: Minghui63 flag leaf, score: 17.373 | N | N | N | N |