| Variant ID: vg0503844669 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr05 | Position: 3844669 |
| Reference Allele: T | Alternative Allele: TAA,TA,TAAA |
| Primary Allele: T | Secondary Allele: TAA |
Inferred Ancestral Allele: Not determined.
GTTATGAAAAAAGTCTCAATTTTTTTTACAATATTCATACAACATACATATACCACTTCATAAAATCCTAAGGCTTAATTCAACTCACACATTTTCGAAA[T/TAA,TA,TAAA]
AAAAAAAGACAAATCCAACATACCCAAATTTATCATTTTTTATTTCTCAAAGTATAGATCGAGTTTCAATTTGATTTTTGTTGGGGTGATAGATATTTCA
TGAAATATCTATCACCCCAACAAAAATCAAATTGAAACTCGATCTATACTTTGAGAAATAAAAAATGATAAATTTGGGTATGTTGGATTTGTCTTTTTTT[A/TTA,TA,TTTA]
TTTCGAAAATGTGTGAGTTGAATTAAGCCTTAGGATTTTATGAAGTGGTATATGTATGTTGTATGAATATTGTAAAAAAAATTGAGACTTTTTTCATAAC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of TAA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 92.50% | 5.50% | 0.11% | 0.00% | TA: 1.86%; TAAA: 0.02% |
| All Indica | 2759 | 98.70% | 1.00% | 0.04% | 0.00% | TA: 0.22% |
| All Japonica | 1512 | 99.30% | 0.30% | 0.07% | 0.00% | TA: 0.40% |
| Aus | 269 | 15.20% | 84.00% | 0.37% | 0.00% | TAAA: 0.37% |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.60% | 0.80% | 0.11% | 0.00% | TA: 0.55% |
| Indica Intermediate | 786 | 97.30% | 2.50% | 0.00% | 0.00% | TA: 0.13% |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.13% | 0.00% | TA: 0.26% |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.10% | 1.20% | 0.00% | 0.00% | TA: 1.66% |
| VI/Aromatic | 96 | 18.80% | 2.10% | 2.08% | 0.00% | TA: 77.08% |
| Intermediate | 90 | 95.60% | 2.20% | 0.00% | 0.00% | TA: 2.22% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0503844669 | T -> TAAA | LOC_Os05g07260.1 | downstream_gene_variant ; 1501.0bp to feature; MODIFIER | silent_mutation | Average:27.804; most accessible tissue: Callus, score: 45.271 | N | N | N | N |
| vg0503844669 | T -> TAAA | LOC_Os05g07260.2 | downstream_gene_variant ; 1512.0bp to feature; MODIFIER | silent_mutation | Average:27.804; most accessible tissue: Callus, score: 45.271 | N | N | N | N |
| vg0503844669 | T -> TAAA | LOC_Os05g07260.4 | downstream_gene_variant ; 1512.0bp to feature; MODIFIER | silent_mutation | Average:27.804; most accessible tissue: Callus, score: 45.271 | N | N | N | N |
| vg0503844669 | T -> TAAA | LOC_Os05g07260.3 | downstream_gene_variant ; 1501.0bp to feature; MODIFIER | silent_mutation | Average:27.804; most accessible tissue: Callus, score: 45.271 | N | N | N | N |
| vg0503844669 | T -> TAAA | LOC_Os05g07270.1 | intron_variant ; MODIFIER | silent_mutation | Average:27.804; most accessible tissue: Callus, score: 45.271 | N | N | N | N |
| vg0503844669 | T -> TA | LOC_Os05g07260.1 | downstream_gene_variant ; 1501.0bp to feature; MODIFIER | silent_mutation | Average:27.804; most accessible tissue: Callus, score: 45.271 | N | N | N | N |
| vg0503844669 | T -> TA | LOC_Os05g07260.2 | downstream_gene_variant ; 1512.0bp to feature; MODIFIER | silent_mutation | Average:27.804; most accessible tissue: Callus, score: 45.271 | N | N | N | N |
| vg0503844669 | T -> TA | LOC_Os05g07260.4 | downstream_gene_variant ; 1512.0bp to feature; MODIFIER | silent_mutation | Average:27.804; most accessible tissue: Callus, score: 45.271 | N | N | N | N |
| vg0503844669 | T -> TA | LOC_Os05g07260.3 | downstream_gene_variant ; 1501.0bp to feature; MODIFIER | silent_mutation | Average:27.804; most accessible tissue: Callus, score: 45.271 | N | N | N | N |
| vg0503844669 | T -> TA | LOC_Os05g07270.1 | intron_variant ; MODIFIER | silent_mutation | Average:27.804; most accessible tissue: Callus, score: 45.271 | N | N | N | N |
| vg0503844669 | T -> TAA | LOC_Os05g07260.1 | downstream_gene_variant ; 1501.0bp to feature; MODIFIER | silent_mutation | Average:27.804; most accessible tissue: Callus, score: 45.271 | N | N | N | N |
| vg0503844669 | T -> TAA | LOC_Os05g07260.2 | downstream_gene_variant ; 1512.0bp to feature; MODIFIER | silent_mutation | Average:27.804; most accessible tissue: Callus, score: 45.271 | N | N | N | N |
| vg0503844669 | T -> TAA | LOC_Os05g07260.4 | downstream_gene_variant ; 1512.0bp to feature; MODIFIER | silent_mutation | Average:27.804; most accessible tissue: Callus, score: 45.271 | N | N | N | N |
| vg0503844669 | T -> TAA | LOC_Os05g07260.3 | downstream_gene_variant ; 1501.0bp to feature; MODIFIER | silent_mutation | Average:27.804; most accessible tissue: Callus, score: 45.271 | N | N | N | N |
| vg0503844669 | T -> TAA | LOC_Os05g07270.1 | intron_variant ; MODIFIER | silent_mutation | Average:27.804; most accessible tissue: Callus, score: 45.271 | N | N | N | N |