| Variant ID: vg1101692327 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 1692327 |
| Reference Allele: A | Alternative Allele: C,G |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TGGCGTGCAAGACGATCGCGAAGCGGAAGCTGGCGAACAAGGAGGACGTCGACGACGTCCGCCGCGAGGTGCAGATCATGCACCACCTCTCCGGCCAGCC[A/C,G]
AACATCGTCGACCTCCGCGGCGCCTACGAGGACAAGCACAACGTCCACCTCGTGATGGAGCTCTGCGCCGGCGGCGAGCTCTTCGACCGCATCATCGCGC
GCGCGATGATGCGGTCGAAGAGCTCGCCGCCGGCGCAGAGCTCCATCACGAGGTGGACGTTGTGCTTGTCCTCGTAGGCGCCGCGGAGGTCGACGATGTT[T/G,C]
GGCTGGCCGGAGAGGTGGTGCATGATCTGCACCTCGCGGCGGACGTCGTCGACGTCCTCCTTGTTCGCCAGCTTCCGCTTCGCGATCGTCTTGCACGCCA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.00% | 0.10% | 0.87% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 99.70% | 0.00% | 0.33% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.00% | 1.66% | 0.00% | NA |
| VI/Aromatic | 96 | 59.40% | 5.20% | 35.42% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 0.00% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1101692327 | A -> G | LOC_Os11g04170.1 | synonymous_variant ; p.Pro142Pro; LOW | N | Average:63.181; most accessible tissue: Zhenshan97 panicle, score: 78.302 | N | N | N | N |
| vg1101692327 | A -> G | LOC_Os11g04150.1 | upstream_gene_variant ; 4228.0bp to feature; MODIFIER | N | Average:63.181; most accessible tissue: Zhenshan97 panicle, score: 78.302 | N | N | N | N |
| vg1101692327 | A -> G | LOC_Os11g04160.1 | downstream_gene_variant ; 987.0bp to feature; MODIFIER | N | Average:63.181; most accessible tissue: Zhenshan97 panicle, score: 78.302 | N | N | N | N |
| vg1101692327 | A -> G | LOC_Os11g04174.1 | downstream_gene_variant ; 2145.0bp to feature; MODIFIER | N | Average:63.181; most accessible tissue: Zhenshan97 panicle, score: 78.302 | N | N | N | N |
| vg1101692327 | A -> G | LOC_Os11g04180.1 | downstream_gene_variant ; 4100.0bp to feature; MODIFIER | N | Average:63.181; most accessible tissue: Zhenshan97 panicle, score: 78.302 | N | N | N | N |
| vg1101692327 | A -> C | LOC_Os11g04170.1 | synonymous_variant ; p.Pro142Pro; LOW | synonymous_codon | Average:63.181; most accessible tissue: Zhenshan97 panicle, score: 78.302 | N | N | N | N |