Search for Variation information by Variation ID:
Detailed information for vg0620603073:
| Variant ID: vg0620603073 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 20603073 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GATGCACAAAACGCCGTCGGAAGGAAGAACAATTTTGGATCATATTCTAGAAAATACTTCCTTCATGACGCAATCTGATGAACCCCAACCGGAGGCATAC[G/A]
TGTCCAAAATAGAGGAACCTCTAACGATCGAGCCGCTCACTGAACCATCCACTTCTGCTAGCTCGATTGATGAGAAGGTTGCTAAGCAGCCGTCCGTCGA
Reverse complement sequence
TCGACGGACGGCTGCTTAGCAACCTTCTCATCAATCGAGCTAGCAGAAGTGGATGGTTCAGTGAGCGGCTCGATCGTTAGAGGTTCCTCTATTTTGGACA[C/T]
GTATGCCTCCGGTTGGGGTTCATCAGATTGCGTCATGAAGGAAGTATTTTCTAGAATATGATCCAAAATTGTTCTTCCTTCCGACGGCGTTTTGTGCATC
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 82.70% | 16.00% | 0.08% | 1.18% | NA |
| All Indica | 2759 | 98.80% | 1.10% | 0.04% | 0.07% | NA |
| All Japonica | 1512 | 49.30% | 47.00% | 0.20% | 3.44% | 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 | 97.20% | 2.60% | 0.22% | 0.00% | NA |
| Indica III | 913 | 99.70% | 0.20% | 0.00% | 0.11% | NA |
| Indica Intermediate | 786 | 98.00% | 1.90% | 0.00% | 0.13% | NA |
| Temperate Japonica | 767 | 79.90% | 19.30% | 0.00% | 0.78% | NA |
| Tropical Japonica | 504 | 11.10% | 87.70% | 0.00% | 1.19% | NA |
| Japonica Intermediate | 241 | 32.00% | 50.20% | 1.24% | 16.60% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 78.90% | 18.90% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0620603073 | G -> A | LOC_Os06g35340.1 | missense_variant ; p.Val173Met; MODERATE | nonsynonymous_codon ; V173M | Average:8.04; most accessible tissue: Minghui63 flag leaf, score: 12.986 | benign  |
0.711 |
TOLERATED | 0.05 |
| vg0620603073 | G -> DEL | LOC_Os06g35340.1 | N | frameshift_variant | Average:8.04; most accessible tissue: Minghui63 flag leaf, score: 12.986 | N | N | N | N |