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Detailed information for vg0424677667:
| Variant ID: vg0424677667 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 24677667 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 120. )
Flanking Sequence (100 bp) in Reference Genome:
TAAGCAGCAACTAGCGGAATGGCTAAATCTTACCTTTATTGATAAGTTCTTGAAAGGAATATGCAGCTCACATGGTGTCCGCTGAGTGATGTCATCAACG[G/A]
GACAGGTCGATTCGTCCTGTGTTTGCATGGCGTCCATACTCTGTGATCCTACCTGCCCCGTTGAGGCGCAGCTGCTACGGTTTCCTGACGGGCTCACCAT
Reverse complement sequence
ATGGTGAGCCCGTCAGGAAACCGTAGCAGCTGCGCCTCAACGGGGCAGGTAGGATCACAGAGTATGGACGCCATGCAAACACAGGACGAATCGACCTGTC[C/T]
CGTTGATGACATCACTCAGCGGACACCATGTGAGCTGCATATTCCTTTCAAGAACTTATCAATAAAGGTAAGATTTAGCCATTCCGCTAGTTGCTGCTTA
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 | 14.60% | 0.10% | 3.70% | 81.63% | NA |
| All Indica | 2759 | 1.10% | 0.10% | 0.43% | 98.33% | NA |
| All Japonica | 1512 | 39.30% | 0.00% | 7.87% | 52.84% | NA |
| Aus | 269 | 1.10% | 0.00% | 3.72% | 95.17% | NA |
| Indica I | 595 | 1.70% | 0.00% | 0.34% | 97.98% | NA |
| Indica II | 465 | 0.40% | 0.20% | 0.22% | 99.14% | NA |
| Indica III | 913 | 0.80% | 0.30% | 0.33% | 98.58% | NA |
| Indica Intermediate | 786 | 1.40% | 0.00% | 0.76% | 97.84% | NA |
| Temperate Japonica | 767 | 70.40% | 0.00% | 8.08% | 21.51% | NA |
| Tropical Japonica | 504 | 1.40% | 0.00% | 6.35% | 92.26% | NA |
| Japonica Intermediate | 241 | 19.50% | 0.00% | 10.37% | 70.12% | NA |
| VI/Aromatic | 96 | 52.10% | 0.00% | 28.12% | 19.79% | NA |
| Intermediate | 90 | 12.20% | 1.10% | 7.78% | 78.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0424677667 | G -> DEL | LOC_Os04g41599.1 | N | frameshift_variant | Average:9.515; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| vg0424677667 | G -> A | LOC_Os04g41599.1 | missense_variant ; p.Pro1352Leu; MODERATE | nonsynonymous_codon ; P1352L | Average:9.515; most accessible tissue: Minghui63 panicle, score: 16.27 | benign  |
0.226 |
DELETERIOUS | 0.01 |