| Variant ID: vg1120597392 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 20597392 |
| Reference Allele: T | Alternative Allele: TA |
| Primary Allele: T | Secondary Allele: TA |
Inferred Ancestral Allele: Not determined.
TCGATCCTCAAAGGCTATGTACGCAATCGCGCTCACCCGGAAGGATCAATGATAGAGGGATACACAACTGAAGAGGCAGTCGAGTGTTGTATGGACTACA[T/TA]
AAAGGATGCTAATGCCATTGGCATTCCTGTTCATTGACATGAAGGTAGATTGTCTGGAAGGGGTACTGTTGGTAGGAAGCAGTTCTTCGATAATGATTAC
GTAATCATTATCGAAGAACTGCTTCCTACCAACAGTACCCCTTCCAGACAATCTACCTTCATGTCAATGAACAGGAATGCCAATGGCATTAGCATCCTTT[A/TA]
TGTAGTCCATACAACACTCGACTGCCTCTTCAGTTGTGTATCCCTCTATCATTGATCCTTCCGGGTGAGCGCGATTGCGTACATAGCCTTTGAGGATCGA
| 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 | 27.50% | 0.20% | 29.45% | 42.85% | NA |
| All Indica | 2759 | 24.10% | 0.40% | 29.50% | 46.03% | NA |
| All Japonica | 1512 | 28.20% | 0.00% | 30.69% | 41.07% | NA |
| Aus | 269 | 49.10% | 0.00% | 28.62% | 22.30% | NA |
| Indica I | 595 | 37.60% | 0.30% | 39.33% | 22.69% | NA |
| Indica II | 465 | 17.20% | 0.00% | 24.30% | 58.49% | NA |
| Indica III | 913 | 18.90% | 0.70% | 26.40% | 54.00% | NA |
| Indica Intermediate | 786 | 23.90% | 0.30% | 28.75% | 47.07% | NA |
| Temperate Japonica | 767 | 32.50% | 0.00% | 45.89% | 21.64% | NA |
| Tropical Japonica | 504 | 26.60% | 0.00% | 12.90% | 60.52% | NA |
| Japonica Intermediate | 241 | 18.30% | 0.00% | 19.50% | 62.24% | NA |
| VI/Aromatic | 96 | 46.90% | 0.00% | 8.33% | 44.79% | NA |
| Intermediate | 90 | 33.30% | 0.00% | 32.22% | 34.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1120597392 | T -> TA | LOC_Os11g35140.1 | upstream_gene_variant ; 2735.0bp to feature; MODIFIER | silent_mutation | Average:6.067; most accessible tissue: Zhenshan97 flag leaf, score: 17.069 | N | N | N | N |
| vg1120597392 | T -> TA | LOC_Os11g35130.1 | intron_variant ; MODIFIER | silent_mutation | Average:6.067; most accessible tissue: Zhenshan97 flag leaf, score: 17.069 | N | N | N | N |
| vg1120597392 | T -> DEL | N | N | silent_mutation | Average:6.067; most accessible tissue: Zhenshan97 flag leaf, score: 17.069 | N | N | N | N |