| Variant ID: vg1115080773 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 15080773 |
| Reference Allele: C | Alternative Allele: CA |
| Primary Allele: C | Secondary Allele: CA |
Inferred Ancestral Allele: Not determined.
TCACAACATCTTAGGAATGTTGCTAGAAATTTTGTACGGTCCCGAACTGATCAGGTAATTACAAATCTTCAGCAAGCTGCTATGTTGAAATGATCTTTTG[C/CA]
AAAAAAATTTACAATATGTTTTCCTGCTCATGGTCTGTTTGTAAAAAAAATAATTTCTTATTGTGTATGGCCAAATCCTGTAACAGGCCAGAGGAGAAAA
TTTTCTCCTCTGGCCTGTTACAGGATTTGGCCATACACAATAAGAAATTATTTTTTTTACAAACAGACCATGAGCAGGAAAACATATTGTAAATTTTTTT[G/TG]
CAAAAGATCATTTCAACATAGCAGCTTGCTGAAGATTTGTAATTACCTGATCAGTTCGGGACCGTACAAAATTTCTAGCAACATTCCTAAGATGTTGTGA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of CA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 63.50% | 0.60% | 16.46% | 19.49% | NA |
| All Indica | 2759 | 39.80% | 0.90% | 27.36% | 31.93% | NA |
| All Japonica | 1512 | 98.50% | 0.00% | 0.26% | 1.19% | NA |
| Aus | 269 | 94.40% | 0.00% | 1.86% | 3.72% | NA |
| Indica I | 595 | 31.40% | 0.00% | 18.82% | 49.75% | NA |
| Indica II | 465 | 27.30% | 5.40% | 40.65% | 26.67% | NA |
| Indica III | 913 | 48.00% | 0.00% | 26.51% | 25.52% | NA |
| Indica Intermediate | 786 | 43.90% | 0.10% | 26.97% | 29.01% | NA |
| Temperate Japonica | 767 | 98.60% | 0.00% | 0.13% | 1.30% | NA |
| Tropical Japonica | 504 | 99.00% | 0.00% | 0.40% | 0.60% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.00% | 0.41% | 2.07% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 71.10% | 0.00% | 15.56% | 13.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1115080773 | C -> CA | LOC_Os11g26340.1 | downstream_gene_variant ; 4808.0bp to feature; MODIFIER | silent_mutation | Average:4.876; most accessible tissue: Callus, score: 8.966 | N | N | N | N |
| vg1115080773 | C -> CA | LOC_Os11g26360.1 | downstream_gene_variant ; 2056.0bp to feature; MODIFIER | silent_mutation | Average:4.876; most accessible tissue: Callus, score: 8.966 | N | N | N | N |
| vg1115080773 | C -> CA | LOC_Os11g26350.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.876; most accessible tissue: Callus, score: 8.966 | N | N | N | N |
| vg1115080773 | C -> DEL | N | N | silent_mutation | Average:4.876; most accessible tissue: Callus, score: 8.966 | N | N | N | N |