| Variant ID: vg1213095955 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr12 | Position: 13095955 |
| Reference Allele: T | Alternative Allele: TAA,TGA |
| Primary Allele: TAA | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 363. )
CAATTAAAATGTTAAACATGCACACATTATTTGCCAAAATCGCTGAACATGAACAGTATAAATGGTAACGTTGTGCACGTATCTTCGTACCAAAACATGT[T/TAA,TGA]
AACTTCTGAAGATGGTGATATAAATTAGATACTCCTACCTTCTTGTCTTTGGGGAAATCGATGGACTGCAGGTACGCCACATATGCGAACGACGAAGCGA
TCGCTTCGTCGTTCGCATATGTGGCGTACCTGCAGTCCATCGATTTCCCCAAAGACAAGAAGGTAGGAGTATCTAATTTATATCACCATCTTCAGAAGTT[A/TTA,TCA]
ACATGTTTTGGTACGAAGATACGTGCACAACGTTACCATTTATACTGTTCATGTTCAGCGATTTTGGCAAATAATGTGTGCATGTTTAACATTTTAATTG
| Populations | Population Size | Frequency of TAA(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 71.20% | 16.10% | 0.28% | 12.42% | TGA: 0.02% |
| All Indica | 2759 | 76.50% | 3.40% | 0.40% | 19.68% | TGA: 0.04% |
| All Japonica | 1512 | 54.20% | 43.00% | 0.13% | 2.71% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.00% | 0.70% | 0.00% | 1.34% | NA |
| Indica II | 465 | 52.30% | 2.80% | 0.86% | 44.09% | NA |
| Indica III | 913 | 77.40% | 3.20% | 0.11% | 19.17% | TGA: 0.11% |
| Indica Intermediate | 786 | 73.50% | 6.00% | 0.76% | 19.72% | NA |
| Temperate Japonica | 767 | 17.70% | 77.20% | 0.26% | 4.82% | NA |
| Tropical Japonica | 504 | 99.00% | 0.60% | 0.00% | 0.40% | NA |
| Japonica Intermediate | 241 | 76.30% | 22.80% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 75.60% | 21.10% | 0.00% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1213095955 | T -> DEL | N | N | silent_mutation | Average:59.508; most accessible tissue: Minghui63 flower, score: 73.172 | N | N | N | N |
| vg1213095955 | T -> TGA | LOC_Os12g23160.1 | upstream_gene_variant ; 2892.0bp to feature; MODIFIER | silent_mutation | Average:59.508; most accessible tissue: Minghui63 flower, score: 73.172 | N | N | N | N |
| vg1213095955 | T -> TGA | LOC_Os12g23170.1 | upstream_gene_variant ; 3692.0bp to feature; MODIFIER | silent_mutation | Average:59.508; most accessible tissue: Minghui63 flower, score: 73.172 | N | N | N | N |
| vg1213095955 | T -> TGA | LOC_Os12g23150.1 | intron_variant ; MODIFIER | silent_mutation | Average:59.508; most accessible tissue: Minghui63 flower, score: 73.172 | N | N | N | N |
| vg1213095955 | T -> TAA | LOC_Os12g23160.1 | upstream_gene_variant ; 2892.0bp to feature; MODIFIER | silent_mutation | Average:59.508; most accessible tissue: Minghui63 flower, score: 73.172 | N | N | N | N |
| vg1213095955 | T -> TAA | LOC_Os12g23170.1 | upstream_gene_variant ; 3692.0bp to feature; MODIFIER | silent_mutation | Average:59.508; most accessible tissue: Minghui63 flower, score: 73.172 | N | N | N | N |
| vg1213095955 | T -> TAA | LOC_Os12g23150.1 | intron_variant ; MODIFIER | silent_mutation | Average:59.508; most accessible tissue: Minghui63 flower, score: 73.172 | N | N | N | N |