| Variant ID: vg0503844372 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr05 | Position: 3844372 |
| Reference Allele: T | Alternative Allele: TTA,TTAA,TTTAA |
| Primary Allele: T | Secondary Allele: TTA |
Inferred Ancestral Allele: Not determined.
AGGAGGGCCAACTAGTTAATTAATGTGTTTCACCATCACATTATAGATTTCATAAGAGATGTACTAGGATTGTGGGAGTACTTCTCAATTTCGTTTTTTT[T/TTA,TTAA,TTTAA]
TAAAAAAAATGCACTTTTGAACATTAACTGTTGTCTTGAGCATAAACATGCAAAATGTGTATAACCAAGAATATATGATCTTCCTAGTAATGGTGCTCAA
TTGAGCACCATTACTAGGAAGATCATATATTCTTGGTTATACACATTTTGCATGTTTATGCTCAAGACAACAGTTAATGTTCAAAAGTGCATTTTTTTTA[A/TAA,TTAA,TTAAA]
AAAAAAACGAAATTGAGAAGTACTCCCACAATCCTAGTACATCTCTTATGAAATCTATAATGTGATGGTGAAACACATTAATTAACTAGTTGGCCCTCCT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of TTA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 58.20% | 1.20% | 32.80% | 6.92% | TTAA: 0.66%; TTTAA: 0.15% |
| All Indica | 2759 | 42.10% | 0.00% | 46.86% | 9.64% | TTAA: 1.12%; TTTAA: 0.25% |
| All Japonica | 1512 | 95.20% | 3.80% | 0.93% | 0.13% | NA |
| Aus | 269 | 25.30% | 0.00% | 54.65% | 20.07% | NA |
| Indica I | 595 | 27.20% | 0.00% | 63.36% | 8.40% | TTTAA: 0.67%; TTAA: 0.34% |
| Indica II | 465 | 49.20% | 0.00% | 40.22% | 10.54% | NA |
| Indica III | 913 | 47.00% | 0.00% | 41.95% | 10.41% | TTAA: 0.66% |
| Indica Intermediate | 786 | 43.40% | 0.10% | 44.02% | 9.16% | TTAA: 2.93%; TTTAA: 0.38% |
| Temperate Japonica | 767 | 98.60% | 0.70% | 0.78% | 0.00% | NA |
| Tropical Japonica | 504 | 97.40% | 2.20% | 0.20% | 0.20% | NA |
| Japonica Intermediate | 241 | 79.70% | 17.00% | 2.90% | 0.41% | NA |
| VI/Aromatic | 96 | 17.70% | 0.00% | 82.29% | 0.00% | NA |
| Intermediate | 90 | 74.40% | 1.10% | 18.89% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0503844372 | T -> DEL | N | N | silent_mutation | Average:55.244; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844372 | T -> TTA | LOC_Os05g07260.1 | downstream_gene_variant ; 1204.0bp to feature; MODIFIER | silent_mutation | Average:55.244; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844372 | T -> TTA | LOC_Os05g07260.2 | downstream_gene_variant ; 1215.0bp to feature; MODIFIER | silent_mutation | Average:55.244; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844372 | T -> TTA | LOC_Os05g07260.4 | downstream_gene_variant ; 1215.0bp to feature; MODIFIER | silent_mutation | Average:55.244; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844372 | T -> TTA | LOC_Os05g07260.3 | downstream_gene_variant ; 1204.0bp to feature; MODIFIER | silent_mutation | Average:55.244; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844372 | T -> TTA | LOC_Os05g07270.1 | intron_variant ; MODIFIER | silent_mutation | Average:55.244; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844372 | T -> TTTAA | LOC_Os05g07260.1 | downstream_gene_variant ; 1204.0bp to feature; MODIFIER | silent_mutation | Average:55.244; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844372 | T -> TTTAA | LOC_Os05g07260.2 | downstream_gene_variant ; 1215.0bp to feature; MODIFIER | silent_mutation | Average:55.244; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844372 | T -> TTTAA | LOC_Os05g07260.4 | downstream_gene_variant ; 1215.0bp to feature; MODIFIER | silent_mutation | Average:55.244; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844372 | T -> TTTAA | LOC_Os05g07260.3 | downstream_gene_variant ; 1204.0bp to feature; MODIFIER | silent_mutation | Average:55.244; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844372 | T -> TTTAA | LOC_Os05g07270.1 | intron_variant ; MODIFIER | silent_mutation | Average:55.244; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844372 | T -> TTAA | LOC_Os05g07260.1 | downstream_gene_variant ; 1204.0bp to feature; MODIFIER | silent_mutation | Average:55.244; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844372 | T -> TTAA | LOC_Os05g07260.2 | downstream_gene_variant ; 1215.0bp to feature; MODIFIER | silent_mutation | Average:55.244; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844372 | T -> TTAA | LOC_Os05g07260.4 | downstream_gene_variant ; 1215.0bp to feature; MODIFIER | silent_mutation | Average:55.244; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844372 | T -> TTAA | LOC_Os05g07260.3 | downstream_gene_variant ; 1204.0bp to feature; MODIFIER | silent_mutation | Average:55.244; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844372 | T -> TTAA | LOC_Os05g07270.1 | intron_variant ; MODIFIER | silent_mutation | Average:55.244; most accessible tissue: Callus, score: 68.266 | N | N | N | N |