| Variant ID: vg0213362446 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 13362446 |
| Reference Allele: T | Alternative Allele: C,TC,TCC |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TGACAGCCAAAAGCAAGCTCAACATTGCAATGGGGAAATTGCGATTAGGGAAATCTTGCCCGTGATTGCAATTTCGGAACAAAATTTTCAAAATTTTGCC[T/C,TC,TCC]
CCCCCCCCACCGGCAAGCATATATCTCACCCGAAATTTCTCCTTTTTTCATGTTTTTGTGAATTTGGTCAAAGTTTATTCTAAATCATTCAAAATTCGTC
GACGAATTTTGAATGATTTAGAATAAACTTTGACCAAATTCACAAAAACATGAAAAAAGGAGAAATTTCGGGTGAGATATATGCTTGCCGGTGGGGGGGG[A/G,GA,GGA]
GGCAAAATTTTGAAAATTTTGTTCCGAAATTGCAATCACGGGCAAGATTTCCCTAATCGCAATTTCCCCATTGCAATGTTGAGCTTGCTTTTGGCTGTCA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 30.80% | 23.40% | 34.85% | 7.89% | TC: 2.96%; TCC: 0.13% |
| All Indica | 2759 | 1.30% | 30.20% | 55.24% | 13.23% | TC: 0.04% |
| All Japonica | 1512 | 86.60% | 0.60% | 3.64% | 0.00% | TC: 8.80%; TCC: 0.33% |
| Aus | 269 | 0.40% | 82.20% | 15.99% | 1.49% | NA |
| Indica I | 595 | 0.30% | 27.10% | 63.19% | 9.41% | NA |
| Indica II | 465 | 2.60% | 32.00% | 56.34% | 9.03% | NA |
| Indica III | 913 | 0.80% | 31.30% | 50.38% | 17.42% | TC: 0.11% |
| Indica Intermediate | 786 | 1.90% | 30.20% | 54.20% | 13.74% | NA |
| Temperate Japonica | 767 | 93.40% | 0.30% | 2.61% | 0.00% | TC: 3.52%; TCC: 0.26% |
| Tropical Japonica | 504 | 78.40% | 1.20% | 4.17% | 0.00% | TC: 15.67%; TCC: 0.60% |
| Japonica Intermediate | 241 | 82.60% | 0.40% | 5.81% | 0.00% | TC: 11.20% |
| VI/Aromatic | 96 | 75.00% | 25.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 38.90% | 21.10% | 27.78% | 4.44% | TC: 6.67%; TCC: 1.11% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0213362446 | T -> TCC | LOC_Os02g22374.4 | upstream_gene_variant ; 670.0bp to feature; MODIFIER | silent_mutation | Average:47.332; most accessible tissue: Zhenshan97 flower, score: 65.164 | N | N | N | N |
| vg0213362446 | T -> TCC | LOC_Os02g22370.1 | downstream_gene_variant ; 1795.0bp to feature; MODIFIER | silent_mutation | Average:47.332; most accessible tissue: Zhenshan97 flower, score: 65.164 | N | N | N | N |
| vg0213362446 | T -> TCC | LOC_Os02g22370.3 | downstream_gene_variant ; 4195.0bp to feature; MODIFIER | silent_mutation | Average:47.332; most accessible tissue: Zhenshan97 flower, score: 65.164 | N | N | N | N |
| vg0213362446 | T -> TCC | LOC_Os02g22370.2 | downstream_gene_variant ; 2641.0bp to feature; MODIFIER | silent_mutation | Average:47.332; most accessible tissue: Zhenshan97 flower, score: 65.164 | N | N | N | N |
| vg0213362446 | T -> TCC | LOC_Os02g22374.2 | downstream_gene_variant ; 540.0bp to feature; MODIFIER | silent_mutation | Average:47.332; most accessible tissue: Zhenshan97 flower, score: 65.164 | N | N | N | N |
| vg0213362446 | T -> TCC | LOC_Os02g22374.1 | intron_variant ; MODIFIER | silent_mutation | Average:47.332; most accessible tissue: Zhenshan97 flower, score: 65.164 | N | N | N | N |
| vg0213362446 | T -> TCC | LOC_Os02g22374.3 | intron_variant ; MODIFIER | silent_mutation | Average:47.332; most accessible tissue: Zhenshan97 flower, score: 65.164 | N | N | N | N |
| vg0213362446 | T -> TC | LOC_Os02g22374.4 | upstream_gene_variant ; 670.0bp to feature; MODIFIER | silent_mutation | Average:47.332; most accessible tissue: Zhenshan97 flower, score: 65.164 | N | N | N | N |
| vg0213362446 | T -> TC | LOC_Os02g22370.1 | downstream_gene_variant ; 1795.0bp to feature; MODIFIER | silent_mutation | Average:47.332; most accessible tissue: Zhenshan97 flower, score: 65.164 | N | N | N | N |
| vg0213362446 | T -> TC | LOC_Os02g22370.3 | downstream_gene_variant ; 4195.0bp to feature; MODIFIER | silent_mutation | Average:47.332; most accessible tissue: Zhenshan97 flower, score: 65.164 | N | N | N | N |
| vg0213362446 | T -> TC | LOC_Os02g22370.2 | downstream_gene_variant ; 2641.0bp to feature; MODIFIER | silent_mutation | Average:47.332; most accessible tissue: Zhenshan97 flower, score: 65.164 | N | N | N | N |
| vg0213362446 | T -> TC | LOC_Os02g22374.2 | downstream_gene_variant ; 540.0bp to feature; MODIFIER | silent_mutation | Average:47.332; most accessible tissue: Zhenshan97 flower, score: 65.164 | N | N | N | N |
| vg0213362446 | T -> TC | LOC_Os02g22374.1 | intron_variant ; MODIFIER | silent_mutation | Average:47.332; most accessible tissue: Zhenshan97 flower, score: 65.164 | N | N | N | N |
| vg0213362446 | T -> TC | LOC_Os02g22374.3 | intron_variant ; MODIFIER | silent_mutation | Average:47.332; most accessible tissue: Zhenshan97 flower, score: 65.164 | N | N | N | N |
| vg0213362446 | T -> DEL | N | N | silent_mutation | Average:47.332; most accessible tissue: Zhenshan97 flower, score: 65.164 | N | N | N | N |
| vg0213362446 | T -> C | LOC_Os02g22374.4 | upstream_gene_variant ; 669.0bp to feature; MODIFIER | silent_mutation | Average:47.332; most accessible tissue: Zhenshan97 flower, score: 65.164 | N | N | N | N |
| vg0213362446 | T -> C | LOC_Os02g22370.1 | downstream_gene_variant ; 1794.0bp to feature; MODIFIER | silent_mutation | Average:47.332; most accessible tissue: Zhenshan97 flower, score: 65.164 | N | N | N | N |
| vg0213362446 | T -> C | LOC_Os02g22370.3 | downstream_gene_variant ; 4194.0bp to feature; MODIFIER | silent_mutation | Average:47.332; most accessible tissue: Zhenshan97 flower, score: 65.164 | N | N | N | N |
| vg0213362446 | T -> C | LOC_Os02g22370.2 | downstream_gene_variant ; 2640.0bp to feature; MODIFIER | silent_mutation | Average:47.332; most accessible tissue: Zhenshan97 flower, score: 65.164 | N | N | N | N |
| vg0213362446 | T -> C | LOC_Os02g22374.2 | downstream_gene_variant ; 541.0bp to feature; MODIFIER | silent_mutation | Average:47.332; most accessible tissue: Zhenshan97 flower, score: 65.164 | N | N | N | N |
| vg0213362446 | T -> C | LOC_Os02g22374.1 | intron_variant ; MODIFIER | silent_mutation | Average:47.332; most accessible tissue: Zhenshan97 flower, score: 65.164 | N | N | N | N |
| vg0213362446 | T -> C | LOC_Os02g22374.3 | intron_variant ; MODIFIER | silent_mutation | Average:47.332; most accessible tissue: Zhenshan97 flower, score: 65.164 | N | N | N | N |
Address: Room B111, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural university, Wuhan, 430070, China
Comments or Questions? Please contact us. Our website: http://xielab.ncpgr.cn/