| Variant ID: vg0503844587 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr05 | Position: 3844587 |
| Reference Allele: A | Alternative Allele: AT,ATT |
| Primary Allele: A | Secondary Allele: AT |
Inferred Ancestral Allele: Not determined.
TCGAGCACAAATTAGGGGAAACACCTTTAAACTCTCAAGAAATATCCCTCCTTTCCTCAGACACCATCCAAACATCCAAACAGTTATGAAAAAAGTCTCA[A/AT,ATT]
TTTTTTTTACAATATTCATACAACATACATATACCACTTCATAAAATCCTAAGGCTTAATTCAACTCACACATTTTCGAAATAAAAAAAGACAAATCCAA
TTGGATTTGTCTTTTTTTATTTCGAAAATGTGTGAGTTGAATTAAGCCTTAGGATTTTATGAAGTGGTATATGTATGTTGTATGAATATTGTAAAAAAAA[T/AT,AAT]
TGAGACTTTTTTCATAACTGTTTGGATGTTTGGATGGTGTCTGAGGAAAGGAGGGATATTTCTTGAGAGTTTAAAGGTGTTTCCCCTAATTTGTGCTCGA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of AT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 91.50% | 7.50% | 0.04% | 0.00% | ATT: 0.97% |
| All Indica | 2759 | 97.10% | 1.20% | 0.04% | 0.00% | ATT: 1.63% |
| All Japonica | 1512 | 99.40% | 0.50% | 0.07% | 0.00% | NA |
| Aus | 269 | 15.20% | 84.80% | 0.00% | 0.00% | NA |
| Indica I | 595 | 97.80% | 0.00% | 0.00% | 0.00% | ATT: 2.18% |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.00% | 1.30% | 0.11% | 0.00% | ATT: 0.55% |
| Indica Intermediate | 786 | 93.90% | 2.70% | 0.00% | 0.00% | ATT: 3.44% |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.10% | 2.50% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 19.80% | 80.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 6.70% | 0.00% | 0.00% | ATT: 1.11% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0503844587 | A -> ATT | LOC_Os05g07260.1 | downstream_gene_variant ; 1419.0bp to feature; MODIFIER | silent_mutation | Average:31.923; most accessible tissue: Callus, score: 45.271 | N | N | N | N |
| vg0503844587 | A -> ATT | LOC_Os05g07260.2 | downstream_gene_variant ; 1430.0bp to feature; MODIFIER | silent_mutation | Average:31.923; most accessible tissue: Callus, score: 45.271 | N | N | N | N |
| vg0503844587 | A -> ATT | LOC_Os05g07260.4 | downstream_gene_variant ; 1430.0bp to feature; MODIFIER | silent_mutation | Average:31.923; most accessible tissue: Callus, score: 45.271 | N | N | N | N |
| vg0503844587 | A -> ATT | LOC_Os05g07260.3 | downstream_gene_variant ; 1419.0bp to feature; MODIFIER | silent_mutation | Average:31.923; most accessible tissue: Callus, score: 45.271 | N | N | N | N |
| vg0503844587 | A -> ATT | LOC_Os05g07270.1 | intron_variant ; MODIFIER | silent_mutation | Average:31.923; most accessible tissue: Callus, score: 45.271 | N | N | N | N |
| vg0503844587 | A -> AT | LOC_Os05g07260.1 | downstream_gene_variant ; 1419.0bp to feature; MODIFIER | silent_mutation | Average:31.923; most accessible tissue: Callus, score: 45.271 | N | N | N | N |
| vg0503844587 | A -> AT | LOC_Os05g07260.2 | downstream_gene_variant ; 1430.0bp to feature; MODIFIER | silent_mutation | Average:31.923; most accessible tissue: Callus, score: 45.271 | N | N | N | N |
| vg0503844587 | A -> AT | LOC_Os05g07260.4 | downstream_gene_variant ; 1430.0bp to feature; MODIFIER | silent_mutation | Average:31.923; most accessible tissue: Callus, score: 45.271 | N | N | N | N |
| vg0503844587 | A -> AT | LOC_Os05g07260.3 | downstream_gene_variant ; 1419.0bp to feature; MODIFIER | silent_mutation | Average:31.923; most accessible tissue: Callus, score: 45.271 | N | N | N | N |
| vg0503844587 | A -> AT | LOC_Os05g07270.1 | intron_variant ; MODIFIER | silent_mutation | Average:31.923; most accessible tissue: Callus, score: 45.271 | N | N | N | N |