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Detailed information for vg1117779305:
| Variant ID: vg1117779305 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 17779305 |
| 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: 286. )
Flanking Sequence (100 bp) in Reference Genome:
CCAGCATCGACTCCTCCTCAGGATCCTGCACCGACTCCTCCTCGTGCTCCTACACCTACTCCCCCGCAAGCTCCTCTTCCGGCACCTTCAAAGTCAAGGG[C/G]
CCCCCCAGCTCCACCGCCTGCCCACACAAGGGCAACGAAGAAGGCGAAAGTTGACGCCGCCAAGAACAAGGACCCAGGGTACGATTGCACGCAAGAGGAG
Reverse complement sequence
CTCCTCTTGCGTGCAATCGTACCCTGGGTCCTTGTTCTTGGCGGCGTCAACTTTCGCCTTCTTCGTTGCCCTTGTGTGGGCAGGCGGTGGAGCTGGGGGG[G/C]
CCCTTGACTTTGAAGGTGCCGGAAGAGGAGCTTGCGGGGGAGTAGGTGTAGGAGCACGAGGAGGAGTCGGTGCAGGATCCTGAGGAGGAGTCGATGCTGG
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 | 1.50% | 0.30% | 7.66% | 90.52% | NA |
| All Indica | 2759 | 0.50% | 0.00% | 5.40% | 94.02% | NA |
| All Japonica | 1512 | 3.40% | 0.80% | 9.85% | 85.91% | NA |
| Aus | 269 | 0.40% | 0.00% | 6.32% | 93.31% | NA |
| Indica I | 595 | 0.00% | 0.00% | 3.70% | 96.30% | NA |
| Indica II | 465 | 0.90% | 0.00% | 13.55% | 85.59% | NA |
| Indica III | 913 | 0.80% | 0.10% | 3.07% | 96.06% | NA |
| Indica Intermediate | 786 | 0.50% | 0.00% | 4.58% | 94.91% | NA |
| Temperate Japonica | 767 | 5.00% | 1.30% | 7.43% | 86.31% | NA |
| Tropical Japonica | 504 | 1.00% | 0.40% | 8.53% | 90.08% | NA |
| Japonica Intermediate | 241 | 3.70% | 0.00% | 20.33% | 75.93% | NA |
| VI/Aromatic | 96 | 1.00% | 3.10% | 35.42% | 60.42% | NA |
| Intermediate | 90 | 1.10% | 0.00% | 14.44% | 84.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1117779305 | C -> DEL | LOC_Os11g30552.1 | N | frameshift_variant | Average:8.629; most accessible tissue: Zhenshan97 flag leaf, score: 15.873 | N | N | N | N |
| vg1117779305 | C -> G | LOC_Os11g30552.1 | missense_variant ; p.Ala728Gly; MODERATE | nonsynonymous_codon ; A728G | Average:8.629; most accessible tissue: Zhenshan97 flag leaf, score: 15.873 | benign  |
0.179 |
TOLERATED | 0.17 |