| Variant ID: vg0725680872 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr07 | Position: 25680872 |
| Reference Allele: TA | Alternative Allele: T,TAA,TAAA |
| Primary Allele: TA | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CTAAAAATTAACGAAGCTAGAAAATATCTTCTATGCAATGATGATTACAGAACAGAGTATTTCAAAGGTCCATTCGTTTCATTGACTCGTCCAAGTTCTG[TA/T,TAA,TAAA]
AAAAAAAAATATAAATAGTTCAAATGATCAATATTTCTAAGCAAAAAAAAGATACATTTTTTCTAAAATAAAGCATTAATAAAGCTTTCTAAAATATTGA
TCAATATTTTAGAAAGCTTTATTAATGCTTTATTTTAGAAAAAATGTATCTTTTTTTTGCTTAGAAATATTGATCATTTGAACTATTTATATTTTTTTTT[TA/A,TTA,TTTA]
CAGAACTTGGACGAGTCAATGAAACGAATGGACCTTTGAAATACTCTGTTCTGTAATCATCATTGCATAGAAGATATTTTCTAGCTTCGTTAATTTTTAG
| Populations | Population Size | Frequency of TA(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.50% | 0.30% | 0.15% | 0.00% | TAAA: 0.04%; TAA: 0.02% |
| All Indica | 2759 | 99.70% | 0.10% | 0.14% | 0.00% | TAA: 0.04% |
| All Japonica | 1512 | 99.50% | 0.40% | 0.13% | 0.00% | NA |
| Aus | 269 | 98.50% | 1.10% | 0.37% | 0.00% | NA |
| Indica I | 595 | 99.50% | 0.00% | 0.50% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.70% | 0.20% | 0.00% | 0.00% | TAA: 0.11% |
| Indica Intermediate | 786 | 99.60% | 0.30% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.00% | 0.60% | 0.40% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 2.20% | 0.00% | 0.00% | TAAA: 2.22% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0725680872 | TA -> TAA | LOC_Os07g42895.1 | splice_region_variant&intron_variant ; LOW | N | Average:38.701; most accessible tissue: Zhenshan97 flower, score: 61.872 | N | N | N | N |
| vg0725680872 | TA -> TAA | LOC_Os07g42885.1 | upstream_gene_variant ; 4129.0bp to feature; MODIFIER | N | Average:38.701; most accessible tissue: Zhenshan97 flower, score: 61.872 | N | N | N | N |
| vg0725680872 | TA -> TAA | LOC_Os07g42890.1 | downstream_gene_variant ; 1026.0bp to feature; MODIFIER | N | Average:38.701; most accessible tissue: Zhenshan97 flower, score: 61.872 | N | N | N | N |
| vg0725680872 | TA -> TAA | LOC_Os07g42900.1 | downstream_gene_variant ; 2399.0bp to feature; MODIFIER | N | Average:38.701; most accessible tissue: Zhenshan97 flower, score: 61.872 | N | N | N | N |
| vg0725680872 | TA -> TAA | LOC_Os07g42890.2 | downstream_gene_variant ; 1071.0bp to feature; MODIFIER | N | Average:38.701; most accessible tissue: Zhenshan97 flower, score: 61.872 | N | N | N | N |
| vg0725680872 | TA -> TAAA | LOC_Os07g42895.1 | splice_region_variant&intron_variant ; LOW | N | Average:38.701; most accessible tissue: Zhenshan97 flower, score: 61.872 | N | N | N | N |
| vg0725680872 | TA -> TAAA | LOC_Os07g42885.1 | upstream_gene_variant ; 4129.0bp to feature; MODIFIER | N | Average:38.701; most accessible tissue: Zhenshan97 flower, score: 61.872 | N | N | N | N |
| vg0725680872 | TA -> TAAA | LOC_Os07g42890.1 | downstream_gene_variant ; 1026.0bp to feature; MODIFIER | N | Average:38.701; most accessible tissue: Zhenshan97 flower, score: 61.872 | N | N | N | N |
| vg0725680872 | TA -> TAAA | LOC_Os07g42900.1 | downstream_gene_variant ; 2399.0bp to feature; MODIFIER | N | Average:38.701; most accessible tissue: Zhenshan97 flower, score: 61.872 | N | N | N | N |
| vg0725680872 | TA -> TAAA | LOC_Os07g42890.2 | downstream_gene_variant ; 1071.0bp to feature; MODIFIER | N | Average:38.701; most accessible tissue: Zhenshan97 flower, score: 61.872 | N | N | N | N |
| vg0725680872 | TA -> T | LOC_Os07g42895.1 | splice_region_variant&intron_variant ; LOW | N | Average:38.701; most accessible tissue: Zhenshan97 flower, score: 61.872 | N | N | N | N |
| vg0725680872 | TA -> T | LOC_Os07g42885.1 | upstream_gene_variant ; 4128.0bp to feature; MODIFIER | N | Average:38.701; most accessible tissue: Zhenshan97 flower, score: 61.872 | N | N | N | N |
| vg0725680872 | TA -> T | LOC_Os07g42890.1 | downstream_gene_variant ; 1025.0bp to feature; MODIFIER | N | Average:38.701; most accessible tissue: Zhenshan97 flower, score: 61.872 | N | N | N | N |
| vg0725680872 | TA -> T | LOC_Os07g42900.1 | downstream_gene_variant ; 2400.0bp to feature; MODIFIER | N | Average:38.701; most accessible tissue: Zhenshan97 flower, score: 61.872 | N | N | N | N |
| vg0725680872 | TA -> T | LOC_Os07g42890.2 | downstream_gene_variant ; 1070.0bp to feature; MODIFIER | N | Average:38.701; most accessible tissue: Zhenshan97 flower, score: 61.872 | N | N | N | N |