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Detailed information for vg1117779127:
| Variant ID: vg1117779127 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 17779127 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 313. )
Flanking Sequence (100 bp) in Reference Genome:
TGAGACGCATCTACGAGACACATGCCATGCCATTATTCTATGGCGCAGGCGGTACATCATCCTCCCTGGGCGACAAGCGGCGTCTCGTGCACCATCTCCT[C/T]
CGGCTCCGCCATCTCCTCCTCAGGATCCTGCACCGTCTCCTCCTCATGCTCCGCCAGCACCGTCTCCACCTCAGGCTCCAGCATCGACTCCTCCTCAGGA
Reverse complement sequence
TCCTGAGGAGGAGTCGATGCTGGAGCCTGAGGTGGAGACGGTGCTGGCGGAGCATGAGGAGGAGACGGTGCAGGATCCTGAGGAGGAGATGGCGGAGCCG[G/A]
AGGAGATGGTGCACGAGACGCCGCTTGTCGCCCAGGGAGGATGATGTACCGCCTGCGCCATAGAATAATGGCATGGCATGTGTCTCGTAGATGCGTCTCA
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 | 12.10% | 0.20% | 12.17% | 75.54% | NA |
| All Indica | 2759 | 6.80% | 0.30% | 3.23% | 89.71% | NA |
| All Japonica | 1512 | 19.90% | 0.00% | 29.23% | 50.86% | NA |
| Aus | 269 | 7.40% | 0.00% | 2.23% | 90.33% | NA |
| Indica I | 595 | 4.90% | 0.00% | 1.34% | 93.78% | NA |
| Indica II | 465 | 20.60% | 0.00% | 4.73% | 74.62% | NA |
| Indica III | 913 | 1.40% | 0.80% | 3.29% | 94.52% | NA |
| Indica Intermediate | 786 | 6.20% | 0.10% | 3.69% | 89.95% | NA |
| Temperate Japonica | 767 | 12.60% | 0.00% | 43.55% | 43.81% | NA |
| Tropical Japonica | 504 | 17.90% | 0.00% | 9.92% | 72.22% | NA |
| Japonica Intermediate | 241 | 47.30% | 0.00% | 24.07% | 28.63% | NA |
| VI/Aromatic | 96 | 42.70% | 1.00% | 36.46% | 19.79% | NA |
| Intermediate | 90 | 25.60% | 0.00% | 3.33% | 71.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1117779127 | C -> T | LOC_Os11g30552.1 | missense_variant ; p.Pro669Ser; MODERATE | nonsynonymous_codon ; P669S | Average:7.651; most accessible tissue: Zhenshan97 flag leaf, score: 11.736 | possibly damaging  |
1.531 |
TOLERATED | 0.12 |
| vg1117779127 | C -> DEL | LOC_Os11g30552.1 | N | frameshift_variant | Average:7.651; most accessible tissue: Zhenshan97 flag leaf, score: 11.736 | N | N | N | N |