| Variant ID: vg1101692762 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 1692762 |
| Reference Allele: G | Alternative Allele: A,C |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 241. )
AGGTGCTCAAGAGGAAGTACGGCCCCGAGGCCGACATCTGGAGCATCGGCGTCATGCTCTACATCTTCCTCGCCGGCGTGCCGCCCTTCTGGGCCGAGTC[G/A,C]
GAGAACGCCATCTTCACCGCCATCCTTCGCGGACAGATCGACCTCGCCAGTGAGCCATGGCCGAAGATCTCCTCTGGAGCCAAGGACCTCGTCAGGAAGA
TCTTCCTGACGAGGTCCTTGGCTCCAGAGGAGATCTTCGGCCATGGCTCACTGGCGAGGTCGATCTGTCCGCGAAGGATGGCGGTGAAGATGGCGTTCTC[C/T,G]
GACTCGGCCCAGAAGGGCGGCACGCCGGCGAGGAAGATGTAGAGCATGACGCCGATGCTCCAGATGTCGGCCTCGGGGCCGTACTTCCTCTTGAGCACCT
| 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 | 55.70% | 0.70% | 10.35% | 33.24% | NA |
| All Indica | 2759 | 31.60% | 1.20% | 14.68% | 52.52% | NA |
| All Japonica | 1512 | 98.30% | 0.10% | 0.20% | 1.46% | NA |
| Aus | 269 | 39.80% | 0.00% | 26.39% | 33.83% | NA |
| Indica I | 595 | 35.00% | 3.20% | 24.03% | 37.82% | NA |
| Indica II | 465 | 40.40% | 1.10% | 11.40% | 47.10% | NA |
| Indica III | 913 | 20.30% | 0.10% | 11.28% | 68.35% | NA |
| Indica Intermediate | 786 | 37.20% | 0.90% | 13.49% | 48.47% | NA |
| Temperate Japonica | 767 | 96.70% | 0.10% | 0.26% | 2.87% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 80.00% | 0.00% | 10.00% | 10.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1101692762 | G -> A | LOC_Os11g04170.1 | synonymous_variant ; p.Ser287Ser; LOW | synonymous_codon | Average:68.98; most accessible tissue: Zhenshan97 panicle, score: 87.451 | N | N | N | N |
| vg1101692762 | G -> DEL | LOC_Os11g04170.1 | N | frameshift_variant | Average:68.98; most accessible tissue: Zhenshan97 panicle, score: 87.451 | N | N | N | N |
| vg1101692762 | G -> C | LOC_Os11g04170.1 | synonymous_variant ; p.Ser287Ser; LOW | N | Average:68.98; most accessible tissue: Zhenshan97 panicle, score: 87.451 | N | N | N | N |
| vg1101692762 | G -> C | LOC_Os11g04150.1 | upstream_gene_variant ; 4663.0bp to feature; MODIFIER | N | Average:68.98; most accessible tissue: Zhenshan97 panicle, score: 87.451 | N | N | N | N |
| vg1101692762 | G -> C | LOC_Os11g04160.1 | downstream_gene_variant ; 1422.0bp to feature; MODIFIER | N | Average:68.98; most accessible tissue: Zhenshan97 panicle, score: 87.451 | N | N | N | N |
| vg1101692762 | G -> C | LOC_Os11g04174.1 | downstream_gene_variant ; 1710.0bp to feature; MODIFIER | N | Average:68.98; most accessible tissue: Zhenshan97 panicle, score: 87.451 | N | N | N | N |
| vg1101692762 | G -> C | LOC_Os11g04180.1 | downstream_gene_variant ; 3665.0bp to feature; MODIFIER | N | Average:68.98; most accessible tissue: Zhenshan97 panicle, score: 87.451 | N | N | N | N |