| Variant ID: vg0503844374 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr05 | Position: 3844374 |
| Reference Allele: A | Alternative Allele: AAT,AT,T |
| Primary Allele: AAT | Secondary Allele: A |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, T: 0.02, others allele: 0.00, population size: 104. )
GAGGGCCAACTAGTTAATTAATGTGTTTCACCATCACATTATAGATTTCATAAGAGATGTACTAGGATTGTGGGAGTACTTCTCAATTTCGTTTTTTTTT[A/AAT,AT,T]
AAAAAAATGCACTTTTGAACATTAACTGTTGTCTTGAGCATAAACATGCAAAATGTGTATAACCAAGAATATATGATCTTCCTAGTAATGGTGCTCAAAA
TTTTGAGCACCATTACTAGGAAGATCATATATTCTTGGTTATACACATTTTGCATGTTTATGCTCAAGACAACAGTTAATGTTCAAAAGTGCATTTTTTT[T/ATT,AT,A]
AAAAAAAAACGAAATTGAGAAGTACTCCCACAATCCTAGTACATCTCTTATGAAATCTATAATGTGATGGTGAAACACATTAATTAACTAGTTGGCCCTC
| Populations | Population Size | Frequency of AAT(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 50.50% | 41.00% | 0.30% | 0.04% | AT: 7.60%; T: 0.61% |
| All Indica | 2759 | 83.30% | 14.70% | 0.40% | 0.07% | AT: 1.38%; T: 0.22% |
| All Japonica | 1512 | 1.30% | 97.40% | 0.13% | 0.00% | AT: 0.60%; T: 0.60% |
| Aus | 269 | 10.40% | 0.40% | 0.00% | 0.00% | AT: 84.76%; T: 4.46% |
| Indica I | 595 | 94.60% | 5.00% | 0.34% | 0.00% | NA |
| Indica II | 465 | 74.20% | 24.50% | 1.08% | 0.00% | AT: 0.22% |
| Indica III | 913 | 85.80% | 11.80% | 0.22% | 0.00% | AT: 1.64%; T: 0.55% |
| Indica Intermediate | 786 | 77.10% | 19.50% | 0.25% | 0.25% | AT: 2.80%; T: 0.13% |
| Temperate Japonica | 767 | 1.70% | 98.00% | 0.13% | 0.00% | AT: 0.13% |
| Tropical Japonica | 504 | 0.40% | 97.40% | 0.20% | 0.00% | T: 1.79%; AT: 0.20% |
| Japonica Intermediate | 241 | 1.70% | 95.40% | 0.00% | 0.00% | AT: 2.90% |
| VI/Aromatic | 96 | 10.40% | 7.30% | 0.00% | 0.00% | AT: 82.29% |
| Intermediate | 90 | 34.40% | 56.70% | 1.11% | 0.00% | AT: 5.56%; T: 2.22% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0503844374 | A -> T | LOC_Os05g07260.1 | downstream_gene_variant ; 1205.0bp to feature; MODIFIER | silent_mutation | Average:54.383; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844374 | A -> T | LOC_Os05g07260.2 | downstream_gene_variant ; 1216.0bp to feature; MODIFIER | silent_mutation | Average:54.383; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844374 | A -> T | LOC_Os05g07260.4 | downstream_gene_variant ; 1216.0bp to feature; MODIFIER | silent_mutation | Average:54.383; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844374 | A -> T | LOC_Os05g07260.3 | downstream_gene_variant ; 1205.0bp to feature; MODIFIER | silent_mutation | Average:54.383; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844374 | A -> T | LOC_Os05g07270.1 | intron_variant ; MODIFIER | silent_mutation | Average:54.383; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844374 | A -> DEL | N | N | silent_mutation | Average:54.383; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844374 | A -> AAT | LOC_Os05g07260.1 | downstream_gene_variant ; 1206.0bp to feature; MODIFIER | silent_mutation | Average:54.383; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844374 | A -> AAT | LOC_Os05g07260.2 | downstream_gene_variant ; 1217.0bp to feature; MODIFIER | silent_mutation | Average:54.383; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844374 | A -> AAT | LOC_Os05g07260.4 | downstream_gene_variant ; 1217.0bp to feature; MODIFIER | silent_mutation | Average:54.383; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844374 | A -> AAT | LOC_Os05g07260.3 | downstream_gene_variant ; 1206.0bp to feature; MODIFIER | silent_mutation | Average:54.383; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844374 | A -> AAT | LOC_Os05g07270.1 | intron_variant ; MODIFIER | silent_mutation | Average:54.383; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844374 | A -> AT | LOC_Os05g07260.1 | downstream_gene_variant ; 1206.0bp to feature; MODIFIER | silent_mutation | Average:54.383; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844374 | A -> AT | LOC_Os05g07260.2 | downstream_gene_variant ; 1217.0bp to feature; MODIFIER | silent_mutation | Average:54.383; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844374 | A -> AT | LOC_Os05g07260.4 | downstream_gene_variant ; 1217.0bp to feature; MODIFIER | silent_mutation | Average:54.383; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844374 | A -> AT | LOC_Os05g07260.3 | downstream_gene_variant ; 1206.0bp to feature; MODIFIER | silent_mutation | Average:54.383; most accessible tissue: Callus, score: 68.266 | N | N | N | N |
| vg0503844374 | A -> AT | LOC_Os05g07270.1 | intron_variant ; MODIFIER | silent_mutation | Average:54.383; most accessible tissue: Callus, score: 68.266 | N | N | N | N |