Variant ID: vg0918113312 (JBrowse) | Variation Type: INDEL |
Chromosome: chr09 | Position: 18113312 |
Reference Allele: T | Alternative Allele: TA |
Primary Allele: T | Secondary Allele: TA |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 286. )
TATATAGAATTTGGAACACCTTGGCCCTCATTGGCTCATACTTGATATAGAAATTACTCTGTCATGGTATTTACCTTCTGCTTGTTGTTGCCATGAGAAA[T/TA]
AAAAAAAAATGGCAGTTAAATTCGTGCATTGCATTGTCATGTGCAGAGAAACAGAAATCCAAGTGCACGAACAGAAGATAAACAAATATCAAGCTATACT
AGTATAGCTTGATATTTGTTTATCTTCTGTTCGTGCACTTGGATTTCTGTTTCTCTGCACATGACAATGCAATGCACGAATTTAACTGCCATTTTTTTTT[A/TA]
TTTCTCATGGCAACAACAAGCAGAAGGTAAATACCATGACAGAGTAATTTCTATATCAAGTATGAGCCAATGAGGGCCAAGGTGTTCCAAATTCTATATA
Populations | Population Size | Frequency of T(primary allele) | Frequency of TA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 92.20% | 7.40% | 0.36% | 0.00% | NA |
All Indica | 2759 | 86.80% | 12.60% | 0.58% | 0.00% | NA |
All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 64.00% | 34.30% | 1.68% | 0.00% | NA |
Indica II | 465 | 97.00% | 3.00% | 0.00% | 0.00% | NA |
Indica III | 913 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 83.80% | 15.40% | 0.76% | 0.00% | NA |
Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 96.70% | 2.20% | 1.11% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0918113312 | T -> TA | LOC_Os09g29790.1 | upstream_gene_variant ; 4000.0bp to feature; MODIFIER | silent_mutation | Average:36.525; most accessible tissue: Callus, score: 71.857 | N | N | N | N |
vg0918113312 | T -> TA | LOC_Os09g29810.1 | upstream_gene_variant ; 1812.0bp to feature; MODIFIER | silent_mutation | Average:36.525; most accessible tissue: Callus, score: 71.857 | N | N | N | N |
vg0918113312 | T -> TA | LOC_Os09g29800.1 | intron_variant ; MODIFIER | silent_mutation | Average:36.525; most accessible tissue: Callus, score: 71.857 | N | N | N | N |