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Detailed information for vg0609242768:
| Variant ID: vg0609242768 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 9242768 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 81. )
Flanking Sequence (100 bp) in Reference Genome:
GGTGTTGTGGACGGAGCACCACCTGCCGGCGGGGCGCTCCCTGCCGGGAGTTCCGGCCTCTTTCTTTTTGTCGCTCGCAGGCCTCCCCTTTCGGGTGGCC[C/T]
GCGGAGCGCCCTCGACGGCGAGGACATGACCCTCGTCGCCGGAACGGTCCGACCTCTTCTTCCTCCTCCTATCACGCCGCCCTGTCTGAGCGGCGGATCC
Reverse complement sequence
GGATCCGCCGCTCAGACAGGGCGGCGTGATAGGAGGAGGAAGAAGAGGTCGGACCGTTCCGGCGACGAGGGTCATGTCCTCGCCGTCGAGGGCGCTCCGC[G/A]
GGCCACCCGAAAGGGGAGGCCTGCGAGCGACAAAAAGAAAGAGGCCGGAACTCCCGGCAGGGAGCGCCCCGCCGGCAGGTGGTGCTCCGTCCACAACACC
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 | 3.00% | 0.50% | 7.32% | 89.12% | NA |
| All Indica | 2759 | 0.00% | 0.00% | 0.33% | 99.60% | NA |
| All Japonica | 1512 | 9.30% | 1.60% | 17.66% | 71.43% | NA |
| Aus | 269 | 0.00% | 0.00% | 23.42% | 76.58% | NA |
| Indica I | 595 | 0.20% | 0.00% | 0.00% | 99.83% | NA |
| Indica II | 465 | 0.00% | 0.20% | 0.00% | 99.78% | NA |
| Indica III | 913 | 0.00% | 0.00% | 0.11% | 99.89% | NA |
| Indica Intermediate | 786 | 0.00% | 0.00% | 1.02% | 98.98% | NA |
| Temperate Japonica | 767 | 17.10% | 3.00% | 32.86% | 47.07% | NA |
| Tropical Japonica | 504 | 1.20% | 0.00% | 0.00% | 98.81% | NA |
| Japonica Intermediate | 241 | 1.70% | 0.40% | 6.22% | 91.70% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 2.08% | 97.92% | NA |
| Intermediate | 90 | 1.10% | 0.00% | 5.56% | 93.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0609242768 | C -> T | LOC_Os06g16230.1 | missense_variant ; p.Arg448Gln; MODERATE | nonsynonymous_codon ; R448Q | Average:4.372; most accessible tissue: Minghui63 panicle, score: 7.125 | possibly damaging  |
1.699 |
DELETERIOUS | 0.00 |
| vg0609242768 | C -> DEL | LOC_Os06g16230.1 | N | frameshift_variant | Average:4.372; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |