| Variant ID: vg0521976358 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr05 | Position: 21976358 |
| Reference Allele: TA | Alternative Allele: T |
| Primary Allele: TA | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AAATCAGAAAGAACCCCTCCATTTTAAAAAATGAGTATATACAATCATCTAACAAAGTTCAGAACAAAGCTCCCCATATTTTTTTGTTAGTAGTACAACA[TA/T]
TATTTTTTTAAAATTTGCAGTAAGTACTGATTATAAATTAGGTTGTTTTTTGTAAACTACATTTTCAGTTAGTAGTAGTATATGCTATTTTTAAATATAG
CTATATTTAAAAATAGCATATACTACTACTAACTGAAAATGTAGTTTACAAAAAACAACCTAATTTATAATCAGTACTTACTGCAAATTTTAAAAAAATA[TA/A]
TGTTGTACTACTAACAAAAAAATATGGGGAGCTTTGTTCTGAACTTTGTTAGATGATTGTATATACTCATTTTTTAAAATGGAGGGGTTCTTTCTGATTT
| 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 | 39.20% | 7.00% | 13.20% | 40.63% | NA |
| All Indica | 2759 | 3.60% | 11.50% | 20.73% | 64.12% | NA |
| All Japonica | 1512 | 98.70% | 0.10% | 0.46% | 0.79% | NA |
| Aus | 269 | 45.00% | 1.10% | 13.01% | 40.89% | NA |
| Indica I | 595 | 2.70% | 16.00% | 12.61% | 68.74% | NA |
| Indica II | 465 | 3.40% | 2.80% | 16.99% | 76.77% | NA |
| Indica III | 913 | 2.50% | 14.70% | 27.93% | 54.87% | NA |
| Indica Intermediate | 786 | 5.70% | 9.70% | 20.74% | 63.87% | NA |
| Temperate Japonica | 767 | 98.70% | 0.10% | 0.13% | 1.04% | NA |
| Tropical Japonica | 504 | 99.20% | 0.00% | 0.40% | 0.40% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.00% | 1.66% | 0.83% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 51.10% | 7.80% | 11.11% | 30.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0521976358 | TA -> T | LOC_Os05g37550.1 | downstream_gene_variant ; 3728.0bp to feature; MODIFIER | silent_mutation | Average:5.809; most accessible tissue: Zhenshan97 flower, score: 12.818 | N | N | N | N |
| vg0521976358 | TA -> T | LOC_Os05g37540.1 | intron_variant ; MODIFIER | silent_mutation | Average:5.809; most accessible tissue: Zhenshan97 flower, score: 12.818 | N | N | N | N |
| vg0521976358 | TA -> DEL | N | N | silent_mutation | Average:5.809; most accessible tissue: Zhenshan97 flower, score: 12.818 | N | N | N | N |