| Variant ID: vg1101692951 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 1692951 |
| Reference Allele: CT | Alternative Allele: C,CTT |
| Primary Allele: CT | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TCGTCAGGAAGATGCTCAACATCAACCCCAAGGAGAGGCTTACAGCATTCCAAGTGCTCAGTAAGTTTATTTGTTACAGATTAATTACTCAAATCTGCTC[CT/C,CTT]
TTTTTTTTCATATAGAGGTACAGTTTGGATTAATTTTCCCTTTATTGGTGTCAGAATTAAATTTGGATTCATTTGGATCAATTTGGATTTGCAGATCACC
GGTGATCTGCAAATCCAAATTGATCCAAATGAATCCAAATTTAATTCTGACACCAATAAAGGGAAAATTAATCCAAACTGTACCTCTATATGAAAAAAAA[AG/G,AAG]
GAGCAGATTTGAGTAATTAATCTGTAACAAATAAACTTACTGAGCACTTGGAATGCTGTAAGCCTCTCCTTGGGGTTGATGTTGAGCATCTTCCTGACGA
| Populations | Population Size | Frequency of CT(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 84.40% | 1.20% | 7.38% | 7.00% | NA |
| All Indica | 2759 | 78.50% | 0.90% | 9.75% | 10.87% | NA |
| All Japonica | 1512 | 98.80% | 1.00% | 0.13% | 0.07% | NA |
| Aus | 269 | 60.60% | 0.70% | 27.88% | 10.78% | NA |
| Indica I | 595 | 35.50% | 1.80% | 30.59% | 32.10% | NA |
| Indica II | 465 | 90.80% | 0.20% | 3.23% | 5.81% | NA |
| Indica III | 913 | 98.60% | 0.20% | 0.88% | 0.33% | NA |
| Indica Intermediate | 786 | 80.40% | 1.40% | 8.14% | 10.05% | NA |
| Temperate Japonica | 767 | 99.10% | 0.50% | 0.26% | 0.13% | NA |
| Tropical Japonica | 504 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.10% | 2.90% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 90.60% | 8.30% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 86.70% | 10.00% | 2.22% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1101692951 | CT -> CTT | LOC_Os11g04150.1 | upstream_gene_variant ; 4854.0bp to feature; MODIFIER | N | Average:68.14; most accessible tissue: Zhenshan97 panicle, score: 86.788 | N | N | N | N |
| vg1101692951 | CT -> CTT | LOC_Os11g04160.1 | downstream_gene_variant ; 1613.0bp to feature; MODIFIER | N | Average:68.14; most accessible tissue: Zhenshan97 panicle, score: 86.788 | N | N | N | N |
| vg1101692951 | CT -> CTT | LOC_Os11g04174.1 | downstream_gene_variant ; 1519.0bp to feature; MODIFIER | N | Average:68.14; most accessible tissue: Zhenshan97 panicle, score: 86.788 | N | N | N | N |
| vg1101692951 | CT -> CTT | LOC_Os11g04180.1 | downstream_gene_variant ; 3474.0bp to feature; MODIFIER | N | Average:68.14; most accessible tissue: Zhenshan97 panicle, score: 86.788 | N | N | N | N |
| vg1101692951 | CT -> CTT | LOC_Os11g04170.1 | intron_variant ; MODIFIER | N | Average:68.14; most accessible tissue: Zhenshan97 panicle, score: 86.788 | N | N | N | N |
| vg1101692951 | CT -> DEL | N | N | silent_mutation | Average:68.14; most accessible tissue: Zhenshan97 panicle, score: 86.788 | N | N | N | N |
| vg1101692951 | CT -> C | LOC_Os11g04150.1 | upstream_gene_variant ; 4853.0bp to feature; MODIFIER | silent_mutation | Average:68.14; most accessible tissue: Zhenshan97 panicle, score: 86.788 | N | N | N | N |
| vg1101692951 | CT -> C | LOC_Os11g04160.1 | downstream_gene_variant ; 1612.0bp to feature; MODIFIER | silent_mutation | Average:68.14; most accessible tissue: Zhenshan97 panicle, score: 86.788 | N | N | N | N |
| vg1101692951 | CT -> C | LOC_Os11g04174.1 | downstream_gene_variant ; 1520.0bp to feature; MODIFIER | silent_mutation | Average:68.14; most accessible tissue: Zhenshan97 panicle, score: 86.788 | N | N | N | N |
| vg1101692951 | CT -> C | LOC_Os11g04180.1 | downstream_gene_variant ; 3475.0bp to feature; MODIFIER | silent_mutation | Average:68.14; most accessible tissue: Zhenshan97 panicle, score: 86.788 | N | N | N | N |
| vg1101692951 | CT -> C | LOC_Os11g04170.1 | intron_variant ; MODIFIER | silent_mutation | Average:68.14; most accessible tissue: Zhenshan97 panicle, score: 86.788 | N | N | N | N |