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Detailed information for vg0620603068:
| Variant ID: vg0620603068 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 20603068 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 112. )
Flanking Sequence (100 bp) in Reference Genome:
TCGTTGATGCACAAAACGCCGTCGGAAGGAAGAACAATTTTGGATCATATTCTAGAAAATACTTCCTTCATGACGCAATCTGATGAACCCCAACCGGAGG[C/G]
ATACGTGTCCAAAATAGAGGAACCTCTAACGATCGAGCCGCTCACTGAACCATCCACTTCTGCTAGCTCGATTGATGAGAAGGTTGCTAAGCAGCCGTCC
Reverse complement sequence
GGACGGCTGCTTAGCAACCTTCTCATCAATCGAGCTAGCAGAAGTGGATGGTTCAGTGAGCGGCTCGATCGTTAGAGGTTCCTCTATTTTGGACACGTAT[G/C]
CCTCCGGTTGGGGTTCATCAGATTGCGTCATGAAGGAAGTATTTTCTAGAATATGATCCAAAATTGTTCTTCCTTCCGACGGCGTTTTGTGCATCAACGA
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 74.90% | 23.80% | 0.15% | 1.23% | NA |
| All Indica | 2759 | 72.30% | 27.40% | 0.18% | 0.07% | NA |
| All Japonica | 1512 | 93.50% | 2.80% | 0.13% | 3.57% | NA |
| Aus | 269 | 1.10% | 98.90% | 0.00% | 0.00% | NA |
| Indica I | 595 | 95.50% | 4.50% | 0.00% | 0.00% | NA |
| Indica II | 465 | 68.60% | 31.20% | 0.22% | 0.00% | NA |
| Indica III | 913 | 57.00% | 42.60% | 0.33% | 0.11% | NA |
| Indica Intermediate | 786 | 74.90% | 24.80% | 0.13% | 0.13% | NA |
| Temperate Japonica | 767 | 97.90% | 1.20% | 0.13% | 0.78% | NA |
| Tropical Japonica | 504 | 92.70% | 6.00% | 0.00% | 1.39% | NA |
| Japonica Intermediate | 241 | 81.30% | 1.20% | 0.41% | 17.01% | NA |
| VI/Aromatic | 96 | 58.30% | 41.70% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 76.70% | 21.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0620603068 | C -> G | LOC_Os06g35340.1 | missense_variant ; p.Ala171Gly; MODERATE | nonsynonymous_codon ; A171G | Average:9.91; most accessible tissue: Minghui63 flag leaf, score: 14.81 | benign  |
1.469 |
DELETERIOUS | 0.05 |
| vg0620603068 | C -> DEL | LOC_Os06g35340.1 | N | frameshift_variant | Average:9.91; most accessible tissue: Minghui63 flag leaf, score: 14.81 | N | N | N | N |