| Variant ID: vg0517888122 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr05 | Position: 17888122 |
| Reference Allele: T | Alternative Allele: TC,TCC,TCCC |
| Primary Allele: TC | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 286. )
CAACATACAAACACATGAGGAACAATTAAGACCAACACAGTTCAAGCTCAGGACACAGCTAAATTCCATTCTTCTATAAAAAAAAAGGAGTTCCAATCTT[T/TC,TCC,TCCC]
CCCCCCCAACAACAATATCACCCTGATTCTGCATCCACATTTTACCTCTTCAGCGAATTCCTGCCTCGGCGCCCCAATGCGCTTCTTGATCGCGACGACG
CGTCGTCGCGATCAAGAAGCGCATTGGGGCGCCGAGGCAGGAATTCGCTGAAGAGGTAAAATGTGGATGCAGAATCAGGGTGATATTGTTGTTGGGGGGG[A/GA,GGA,GGGA]
AAGATTGGAACTCCTTTTTTTTTATAGAAGAATGGAATTTAGCTGTGTCCTGAGCTTGAACTGTGTTGGTCTTAATTGTTCCTCATGTGTTTGTATGTTG
| Populations | Population Size | Frequency of TC(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 57.90% | 40.90% | 0.25% | 0.00% | TCC: 0.93%; TCCC: 0.06% |
| All Indica | 2759 | 91.40% | 6.90% | 0.29% | 0.00% | TCC: 1.45%; TCCC: 0.04% |
| All Japonica | 1512 | 7.90% | 91.70% | 0.20% | 0.00% | TCCC: 0.13% |
| Aus | 269 | 20.40% | 78.10% | 0.00% | 0.00% | TCC: 1.49% |
| Indica I | 595 | 99.20% | 0.30% | 0.17% | 0.00% | TCC: 0.34% |
| Indica II | 465 | 73.50% | 25.80% | 0.65% | 0.00% | NA |
| Indica III | 913 | 93.90% | 2.20% | 0.11% | 0.00% | TCC: 3.72%; TCCC: 0.11% |
| Indica Intermediate | 786 | 93.10% | 6.00% | 0.38% | 0.00% | TCC: 0.51% |
| Temperate Japonica | 767 | 3.00% | 97.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 18.30% | 81.00% | 0.40% | 0.00% | TCCC: 0.40% |
| Japonica Intermediate | 241 | 2.10% | 97.50% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 0.00% | 100.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 42.20% | 56.70% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0517888122 | T -> TCCC | LOC_Os05g30830.1 | downstream_gene_variant ; 3846.0bp to feature; MODIFIER | silent_mutation | Average:70.557; most accessible tissue: Zhenshan97 flower, score: 83.392 | N | N | N | N |
| vg0517888122 | T -> TCCC | LOC_Os05g30820.1 | intron_variant ; MODIFIER | silent_mutation | Average:70.557; most accessible tissue: Zhenshan97 flower, score: 83.392 | N | N | N | N |
| vg0517888122 | T -> TCCC | LOC_Os05g30820.2 | intron_variant ; MODIFIER | silent_mutation | Average:70.557; most accessible tissue: Zhenshan97 flower, score: 83.392 | N | N | N | N |
| vg0517888122 | T -> TCC | LOC_Os05g30830.1 | downstream_gene_variant ; 3846.0bp to feature; MODIFIER | silent_mutation | Average:70.557; most accessible tissue: Zhenshan97 flower, score: 83.392 | N | N | N | N |
| vg0517888122 | T -> TCC | LOC_Os05g30820.1 | intron_variant ; MODIFIER | silent_mutation | Average:70.557; most accessible tissue: Zhenshan97 flower, score: 83.392 | N | N | N | N |
| vg0517888122 | T -> TCC | LOC_Os05g30820.2 | intron_variant ; MODIFIER | silent_mutation | Average:70.557; most accessible tissue: Zhenshan97 flower, score: 83.392 | N | N | N | N |
| vg0517888122 | T -> TC | LOC_Os05g30830.1 | downstream_gene_variant ; 3846.0bp to feature; MODIFIER | silent_mutation | Average:70.557; most accessible tissue: Zhenshan97 flower, score: 83.392 | N | N | N | N |
| vg0517888122 | T -> TC | LOC_Os05g30820.1 | intron_variant ; MODIFIER | silent_mutation | Average:70.557; most accessible tissue: Zhenshan97 flower, score: 83.392 | N | N | N | N |
| vg0517888122 | T -> TC | LOC_Os05g30820.2 | intron_variant ; MODIFIER | silent_mutation | Average:70.557; most accessible tissue: Zhenshan97 flower, score: 83.392 | N | N | N | N |