| Variant ID: vg0138754905 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 38754905 |
| Reference Allele: TCTTAACATGTTCAAATTATAC | Alternative Allele: T |
| Primary Allele: TCTTAACATGTTCAAATTAT AC | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GGCAAGAAGGTTGTGTGTGTGTCACAGGAGTTAAGTCAGTTTACATTCTGATGAGTATCAGAAACCTCTCTGAATTGAGGTGATAAGTAATAGATGTTTG[TCTTAACATGTTCAAATTATAC/T]
CTGGGAAAAAAGTTCAATTCGCTCACTCAATACCAGTGAAAATATTAATTACCATTTACCAGGTCATGATTTCGTTCTAAATCAACAAGACCAGCAGATC
GATCTGCTGGTCTTGTTGATTTAGAACGAAATCATGACCTGGTAAATGGTAATTAATATTTTCACTGGTATTGAGTGAGCGAATTGAACTTTTTTCCCAG[GTATAATTTGAACATGTTAAGA/A]
CAAACATCTATTACTTATCACCTCAATTCAGAGAGGTTTCTGATACTCATCAGAATGTAAACTGACTTAACTCCTGTGACACACACACAACCTTCTTGCC
| Populations | Population Size | Frequency of TCTTAACATGTTCAAATTAT AC(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 79.80% | 19.60% | 0.08% | 0.49% | NA |
| All Indica | 2759 | 66.00% | 33.00% | 0.14% | 0.83% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 97.40% | 2.60% | 0.00% | 0.00% | NA |
| Indica I | 595 | 46.20% | 52.90% | 0.00% | 0.84% | NA |
| Indica II | 465 | 97.20% | 2.60% | 0.00% | 0.22% | NA |
| Indica III | 913 | 56.60% | 42.30% | 0.11% | 0.99% | NA |
| Indica Intermediate | 786 | 73.40% | 25.20% | 0.38% | 1.02% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 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 | 90.00% | 10.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0138754905 | TCTTAACATGTTCAAATTATAC -> T | LOC_Os01g66720.1 | 3_prime_UTR_variant ; 53.0bp to feature; MODIFIER | silent_mutation | Average:65.655; most accessible tissue: Zhenshan97 panicle, score: 81.752 | N | N | N | N |
| vg0138754905 | TCTTAACATGTTCAAATTATAC -> T | LOC_Os01g66740.1 | upstream_gene_variant ; 4851.0bp to feature; MODIFIER | silent_mutation | Average:65.655; most accessible tissue: Zhenshan97 panicle, score: 81.752 | N | N | N | N |
| vg0138754905 | TCTTAACATGTTCAAATTATAC -> T | LOC_Os01g66710.1 | downstream_gene_variant ; 4138.0bp to feature; MODIFIER | silent_mutation | Average:65.655; most accessible tissue: Zhenshan97 panicle, score: 81.752 | N | N | N | N |
| vg0138754905 | TCTTAACATGTTCAAATTATAC -> T | LOC_Os01g66730.1 | downstream_gene_variant ; 152.0bp to feature; MODIFIER | silent_mutation | Average:65.655; most accessible tissue: Zhenshan97 panicle, score: 81.752 | N | N | N | N |
| vg0138754905 | TCTTAACATGTTCAAATTATAC -> T | LOC_Os01g66730.2 | downstream_gene_variant ; 180.0bp to feature; MODIFIER | silent_mutation | Average:65.655; most accessible tissue: Zhenshan97 panicle, score: 81.752 | N | N | N | N |
| vg0138754905 | TCTTAACATGTTCAAATTATAC -> DEL | N | N | silent_mutation | Average:65.655; most accessible tissue: Zhenshan97 panicle, score: 81.752 | N | N | N | N |