| Variant ID: vg0524150557 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr05 | Position: 24150557 |
| Reference Allele: T | Alternative Allele: TCAAA,TA,TCAA,TC,TCAAAA,TCAAAAA |
| Primary Allele: T | Secondary Allele: TCAAA |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 263. )
AATTGGTCCTTCAATATTGTTCGAAGCGATTTCCCTAACCCAAGATAGCAAAAGACAGAAAGAGTCAATAAAAACTCCATGTAACTGATGGGCTTGGCAT[T/TCAAA,TA,TCAA,TC,TCAAAA,TCAAAAA]
AAAAAAAAAAAAACTGATGGTCTTGCAACTCTCTACAAAGAGAAGCACTAGCAAATTAAACTACATTGACATTAGTCTGCTAAATGTGCCTTTTCATTTC
GAAATGAAAAGGCACATTTAGCAGACTAATGTCAATGTAGTTTAATTTGCTAGTGCTTCTCTTTGTAGAGAGTTGCAAGACCATCAGTTTTTTTTTTTTT[A/TTTGA,TA,TTGA,GA,TTTTGA,TTTTTGA]
ATGCCAAGCCCATCAGTTACATGGAGTTTTTATTGACTCTTTCTGTCTTTTGCTATCTTGGGTTAGGGAAATCGCTTCGAACAATATTGAAGGACCAATT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of TCAAA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 33.70% | 19.40% | 17.12% | 0.00% | TA: 14.83%; TC: 5.61%; TCAA: 5.16%; TCAAAAA: 2.22%; TCAAAA: 2.01% |
| All Indica | 2759 | 3.90% | 31.90% | 25.66% | 0.00% | TA: 22.33%; TCAA: 7.97%; TCAAAAA: 3.70%; TCAAAA: 3.19%; TC: 1.38% |
| All Japonica | 1512 | 91.30% | 0.30% | 3.37% | 0.00% | TA: 4.89%; TCAAAAA: 0.07%; TCAA: 0.07% |
| Aus | 269 | 3.30% | 6.30% | 11.52% | 0.00% | TC: 70.26%; TCAA: 6.69%; TCAAAA: 1.49%; TCAAAAA: 0.37% |
| Indica I | 595 | 1.30% | 35.50% | 41.51% | 0.00% | TA: 16.30%; TCAA: 4.37%; TCAAAA: 0.50%; TCAAAAA: 0.50% |
| Indica II | 465 | 8.80% | 21.10% | 25.81% | 0.00% | TA: 21.72%; TCAAAAA: 9.03%; TCAA: 8.39%; TCAAAA: 4.30%; TC: 0.86% |
| Indica III | 913 | 4.20% | 37.60% | 15.77% | 0.00% | TA: 25.74%; TCAA: 8.54%; TCAAAA: 3.40%; TCAAAAA: 3.40%; TC: 1.42% |
| Indica Intermediate | 786 | 2.70% | 28.90% | 25.06% | 0.00% | TA: 23.28%; TCAA: 9.80%; TCAAAA: 4.33%; TCAAAAA: 3.31%; TC: 2.67% |
| Temperate Japonica | 767 | 87.60% | 0.00% | 4.69% | 0.00% | TA: 7.69% |
| Tropical Japonica | 504 | 95.40% | 0.80% | 1.79% | 0.00% | TA: 1.59%; TCAAAAA: 0.20%; TCAA: 0.20% |
| Japonica Intermediate | 241 | 94.60% | 0.00% | 2.49% | 0.00% | TA: 2.90% |
| VI/Aromatic | 96 | 60.40% | 0.00% | 1.04% | 0.00% | TC: 34.38%; TA: 4.17% |
| Intermediate | 90 | 38.90% | 17.80% | 20.00% | 0.00% | TA: 7.78%; TC: 5.56%; TCAA: 5.56%; TCAAAA: 3.33%; TCAAAAA: 1.11% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0524150557 | T -> TCAAAAA | LOC_Os05g41240.1 | downstream_gene_variant ; 3175.0bp to feature; MODIFIER | silent_mutation | Average:72.029; most accessible tissue: Callus, score: 93.693 | N | N | N | N |
| vg0524150557 | T -> TCAAAAA | LOC_Os05g41240.3 | downstream_gene_variant ; 3175.0bp to feature; MODIFIER | silent_mutation | Average:72.029; most accessible tissue: Callus, score: 93.693 | N | N | N | N |
| vg0524150557 | T -> TCAAAAA | LOC_Os05g41240.2 | downstream_gene_variant ; 3175.0bp to feature; MODIFIER | silent_mutation | Average:72.029; most accessible tissue: Callus, score: 93.693 | N | N | N | N |
| vg0524150557 | T -> TCAAAAA | LOC_Os05g41230.1 | intron_variant ; MODIFIER | silent_mutation | Average:72.029; most accessible tissue: Callus, score: 93.693 | N | N | N | N |
| vg0524150557 | T -> TCAAA | LOC_Os05g41240.1 | downstream_gene_variant ; 3175.0bp to feature; MODIFIER | silent_mutation | Average:72.029; most accessible tissue: Callus, score: 93.693 | N | N | N | N |
| vg0524150557 | T -> TCAAA | LOC_Os05g41240.3 | downstream_gene_variant ; 3175.0bp to feature; MODIFIER | silent_mutation | Average:72.029; most accessible tissue: Callus, score: 93.693 | N | N | N | N |
| vg0524150557 | T -> TCAAA | LOC_Os05g41240.2 | downstream_gene_variant ; 3175.0bp to feature; MODIFIER | silent_mutation | Average:72.029; most accessible tissue: Callus, score: 93.693 | N | N | N | N |
| vg0524150557 | T -> TCAAA | LOC_Os05g41230.1 | intron_variant ; MODIFIER | silent_mutation | Average:72.029; most accessible tissue: Callus, score: 93.693 | N | N | N | N |
| vg0524150557 | T -> TA | LOC_Os05g41240.1 | downstream_gene_variant ; 3175.0bp to feature; MODIFIER | silent_mutation | Average:72.029; most accessible tissue: Callus, score: 93.693 | N | N | N | N |
| vg0524150557 | T -> TA | LOC_Os05g41240.3 | downstream_gene_variant ; 3175.0bp to feature; MODIFIER | silent_mutation | Average:72.029; most accessible tissue: Callus, score: 93.693 | N | N | N | N |
| vg0524150557 | T -> TA | LOC_Os05g41240.2 | downstream_gene_variant ; 3175.0bp to feature; MODIFIER | silent_mutation | Average:72.029; most accessible tissue: Callus, score: 93.693 | N | N | N | N |
| vg0524150557 | T -> TA | LOC_Os05g41230.1 | intron_variant ; MODIFIER | silent_mutation | Average:72.029; most accessible tissue: Callus, score: 93.693 | N | N | N | N |
| vg0524150557 | T -> TCAAAA | LOC_Os05g41240.1 | downstream_gene_variant ; 3175.0bp to feature; MODIFIER | silent_mutation | Average:72.029; most accessible tissue: Callus, score: 93.693 | N | N | N | N |
| vg0524150557 | T -> TCAAAA | LOC_Os05g41240.3 | downstream_gene_variant ; 3175.0bp to feature; MODIFIER | silent_mutation | Average:72.029; most accessible tissue: Callus, score: 93.693 | N | N | N | N |
| vg0524150557 | T -> TCAAAA | LOC_Os05g41240.2 | downstream_gene_variant ; 3175.0bp to feature; MODIFIER | silent_mutation | Average:72.029; most accessible tissue: Callus, score: 93.693 | N | N | N | N |
| vg0524150557 | T -> TCAAAA | LOC_Os05g41230.1 | intron_variant ; MODIFIER | silent_mutation | Average:72.029; most accessible tissue: Callus, score: 93.693 | N | N | N | N |
| vg0524150557 | T -> TCAA | LOC_Os05g41240.1 | downstream_gene_variant ; 3175.0bp to feature; MODIFIER | silent_mutation | Average:72.029; most accessible tissue: Callus, score: 93.693 | N | N | N | N |
| vg0524150557 | T -> TCAA | LOC_Os05g41240.3 | downstream_gene_variant ; 3175.0bp to feature; MODIFIER | silent_mutation | Average:72.029; most accessible tissue: Callus, score: 93.693 | N | N | N | N |
| vg0524150557 | T -> TCAA | LOC_Os05g41240.2 | downstream_gene_variant ; 3175.0bp to feature; MODIFIER | silent_mutation | Average:72.029; most accessible tissue: Callus, score: 93.693 | N | N | N | N |
| vg0524150557 | T -> TCAA | LOC_Os05g41230.1 | intron_variant ; MODIFIER | silent_mutation | Average:72.029; most accessible tissue: Callus, score: 93.693 | N | N | N | N |
| vg0524150557 | T -> TC | LOC_Os05g41240.1 | downstream_gene_variant ; 3175.0bp to feature; MODIFIER | silent_mutation | Average:72.029; most accessible tissue: Callus, score: 93.693 | N | N | N | N |
| vg0524150557 | T -> TC | LOC_Os05g41240.3 | downstream_gene_variant ; 3175.0bp to feature; MODIFIER | silent_mutation | Average:72.029; most accessible tissue: Callus, score: 93.693 | N | N | N | N |
| vg0524150557 | T -> TC | LOC_Os05g41240.2 | downstream_gene_variant ; 3175.0bp to feature; MODIFIER | silent_mutation | Average:72.029; most accessible tissue: Callus, score: 93.693 | N | N | N | N |
| vg0524150557 | T -> TC | LOC_Os05g41230.1 | intron_variant ; MODIFIER | silent_mutation | Average:72.029; most accessible tissue: Callus, score: 93.693 | N | N | N | N |