Variant ID: vg0121350108 (JBrowse) | Variation Type: INDEL |
Chromosome: chr01 | Position: 21350108 |
Reference Allele: TG | Alternative Allele: T |
Primary Allele: TG | Secondary Allele: T |
Inferred Ancestral Allele : TG (evidence from allele frequency in Oryza rufipogon: TG: 1.00, T: 0.00, others allele: 0.00, population size: 227. )
TGGCTTTGCGAAGTGGACCGTTCAAGAGGCGCCTGGGGAACGGTTTGATTGGCTGGAAATGAAGGGGTTCTACTGCTGCGAGGCACAAGGTGCGTATAGT[TG/T]
AAAAGAGTAAAAAGGTACACAACTGCAAAAATCAGCTCGGTCTACAACCGCTTAAAATTACGTTCCGTCCTTATATATAGATTCATTTGTTTCTACCTTA
TAAGGTAGAAACAAATGAATCTATATATAAGGACGGAACGTAATTTTAAGCGGTTGTAGACCGAGCTGATTTTTGCAGTTGTGTACCTTTTTACTCTTTT[CA/A]
ACTATACGCACCTTGTGCCTCGCAGCAGTAGAACCCCTTCATTTCCAGCCAATCAAACCGTTCCCCAGGCGCCTCTTGAACGGTCCACTTCGCAAAGCCA
Populations | Population Size | Frequency of TG(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 98.70% | 1.20% | 0.02% | 0.00% | NA |
All Indica | 2759 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 98.30% | 1.70% | 0.07% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 96.30% | 3.70% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 96.60% | 3.30% | 0.13% | 0.00% | NA |
Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
Intermediate | 90 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0121350108 | TG -> T | LOC_Os01g38120.1 | upstream_gene_variant ; 435.0bp to feature; MODIFIER | silent_mutation | Average:75.691; most accessible tissue: Zhenshan97 root, score: 83.751 | N | N | N | N |
vg0121350108 | TG -> T | LOC_Os01g38140.1 | upstream_gene_variant ; 4361.0bp to feature; MODIFIER | silent_mutation | Average:75.691; most accessible tissue: Zhenshan97 root, score: 83.751 | N | N | N | N |
vg0121350108 | TG -> T | LOC_Os01g38130.1 | intron_variant ; MODIFIER | silent_mutation | Average:75.691; most accessible tissue: Zhenshan97 root, score: 83.751 | N | N | N | N |