| Variant ID: vg0905620942 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr09 | Position: 5620942 |
| Reference Allele: TCTTCCTCTGGAATAGCTGGCTCTC | Alternative Allele: T |
| Primary Allele: TCTTCCTCTGGAATAGCTGG CTCTC | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TGCGTCGGAGCGAAGAGATGGATCTTCTTCCTCTGGAATAGCTGGCAACGATCTAACGAGGCACTAATCCCGCCTTGCGTCGAAGCGAAGAGATGGATCT[TCTTCCTCTGGAATAGCTGGCTCTC/T]
TTTCTTCTGGATCTTCCTCCTCTGGGGTAGCTGACGGCGGTGCTTCTCCCTTGAGCTCGGCCAGTTCCTTCTGCAGGCGATACACCTTGCTTTCTAGCTT
AAGCTAGAAAGCAAGGTGTATCGCCTGCAGAAGGAACTGGCCGAGCTCAAGGGAGAAGCACCGCCGTCAGCTACCCCAGAGGAGGAAGATCCAGAAGAAA[GAGAGCCAGCTATTCCAGAGGAAGA/A]
AGATCCATCTCTTCGCTTCGACGCAAGGCGGGATTAGTGCCTCGTTAGATCGTTGCCAGCTATTCCAGAGGAAGAAGATCCATCTCTTCGCTCCGACGCA
| Populations | Population Size | Frequency of TCTTCCTCTGGAATAGCTGG CTCTC(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.90% | 1.30% | 0.72% | 0.00% | NA |
| All Indica | 2759 | 96.50% | 2.30% | 1.20% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.37% | 0.00% | NA |
| Indica I | 595 | 95.50% | 2.90% | 1.68% | 0.00% | NA |
| Indica II | 465 | 96.60% | 2.20% | 1.29% | 0.00% | NA |
| Indica III | 913 | 97.50% | 1.60% | 0.88% | 0.00% | NA |
| Indica Intermediate | 786 | 96.20% | 2.70% | 1.15% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0905620942 | TCTTCCTCTGGAATAGCTGGCTCTC -> T | LOC_Os09g10310.1 | disruptive_inframe_deletion ; p.Arg188_Glu196delinsLys; MODERATE | N | Average:52.93; most accessible tissue: Zhenshan97 flag leaf, score: 65.82 | N | N | N | N |
| vg0905620942 | TCTTCCTCTGGAATAGCTGGCTCTC -> T | LOC_Os09g10320.1 | upstream_gene_variant ; 3150.0bp to feature; MODIFIER | N | Average:52.93; most accessible tissue: Zhenshan97 flag leaf, score: 65.82 | N | N | N | N |
| vg0905620942 | TCTTCCTCTGGAATAGCTGGCTCTC -> T | LOC_Os09g10330.1 | upstream_gene_variant ; 4532.0bp to feature; MODIFIER | N | Average:52.93; most accessible tissue: Zhenshan97 flag leaf, score: 65.82 | N | N | N | N |