| Variant ID: vg1213914083 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr12 | Position: 13914083 |
| Reference Allele: A | Alternative Allele: AATAT |
| Primary Allele: A | Secondary Allele: AATAT |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 127. )
GGTATCGTCTTAATTCCATCAGCCTTCCATTGATGCATTACATACTGGAATACATACCGTTTGCCGCAATTTCGAAATGATCCTGCATTGAGGCGGATTC[A/AATAT]
ATACATGTATATATGATGTGCAGGGAGCAAACAGGGCCTCGTGACGATGAACATCCCGACGTACAGCAAGAAAGATGTGGCTCTGACGGCGGACTCAGTG
CACTGAGTCCGCCGTCAGAGCCACATCTTTCTTGCTGTACGTCGGGATGTTCATCGTCACGAGGCCCTGTTTGCTCCCTGCACATCATATATACATGTAT[T/ATATT]
GAATCCGCCTCAATGCAGGATCATTTCGAAATTGCGGCAAACGGTATGTATTCCAGTATGTAATGCATCAATGGAAGGCTGATGGAATTAAGACGATACC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of AATAT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 87.00% | 12.50% | 0.13% | 0.34% | NA |
| All Indica | 2759 | 79.60% | 19.80% | 0.18% | 0.51% | NA |
| All Japonica | 1512 | 97.10% | 2.80% | 0.07% | 0.07% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.20% | 1.70% | 0.17% | 0.00% | NA |
| Indica II | 465 | 53.50% | 45.20% | 0.22% | 1.08% | NA |
| Indica III | 913 | 82.10% | 17.10% | 0.11% | 0.66% | NA |
| Indica Intermediate | 786 | 77.90% | 21.50% | 0.25% | 0.38% | NA |
| Temperate Japonica | 767 | 94.80% | 5.20% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.80% | 0.41% | 0.41% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 4.40% | 0.00% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1213914083 | A -> DEL | N | N | silent_mutation | Average:72.169; most accessible tissue: Zhenshan97 young leaf, score: 88.387 | N | N | N | N |
| vg1213914083 | A -> AATAT | LOC_Os12g24400.1 | upstream_gene_variant ; 3327.0bp to feature; MODIFIER | silent_mutation | Average:72.169; most accessible tissue: Zhenshan97 young leaf, score: 88.387 | N | N | N | N |
| vg1213914083 | A -> AATAT | LOC_Os12g24390.1 | intron_variant ; MODIFIER | silent_mutation | Average:72.169; most accessible tissue: Zhenshan97 young leaf, score: 88.387 | N | N | N | N |