| Variant ID: vg0522745784 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr05 | Position: 22745784 |
| Reference Allele: CATAATGCTATTGCT | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: CATAATGCTATTGCT |
Inferred Ancestral Allele: Not determined.
ACCAGCTCGTGATATCTCTTCTGGTCTTTAAACATCGGCATTGCCTGAAAAATATGCAATGCAGATCGCAATTCACAAAGATGCCATTAGCAAACTGAAT[CATAATGCTATTGCT/C]
ATAATGCTATTGCATCTTTCATAATTTCTTTGGGAGAAATGTTGCATTATTTCTGTTCAAAATGCAAAGGTTTTTAAATTCAGATTTCGGCATGCAGAAT
ATTCTGCATGCCGAAATCTGAATTTAAAAACCTTTGCATTTTGAACAGAAATAATGCAACATTTCTCCCAAAGAAATTATGAAAGATGCAATAGCATTAT[AGCAATAGCATTATG/G]
ATTCAGTTTGCTAATGGCATCTTTGTGAATTGCGATCTGCATTGCATATTTTTCAGGCAATGCCGATGTTTAAAGACCAGAAGAGATATCACGAGCTGGT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of CATAATGCTATTGCT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 65.20% | 34.60% | 0.06% | 0.13% | NA |
| All Indica | 2759 | 97.50% | 2.30% | 0.04% | 0.18% | NA |
| All Japonica | 1512 | 3.80% | 96.20% | 0.00% | 0.00% | NA |
| Aus | 269 | 96.30% | 3.30% | 0.00% | 0.37% | NA |
| Indica I | 595 | 97.10% | 2.70% | 0.00% | 0.17% | NA |
| Indica II | 465 | 96.80% | 3.00% | 0.22% | 0.00% | NA |
| Indica III | 913 | 99.10% | 0.80% | 0.00% | 0.11% | NA |
| Indica Intermediate | 786 | 96.30% | 3.30% | 0.00% | 0.38% | NA |
| Temperate Japonica | 767 | 0.50% | 99.50% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 9.10% | 90.90% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 2.90% | 97.10% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 26.00% | 74.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 57.80% | 40.00% | 2.22% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0522745784 | CATAATGCTATTGCT -> DEL | N | N | silent_mutation | Average:42.946; most accessible tissue: Callus, score: 77.168 | N | N | N | N |
| vg0522745784 | CATAATGCTATTGCT -> C | LOC_Os05g38760.1 | upstream_gene_variant ; 1333.0bp to feature; MODIFIER | silent_mutation | Average:42.946; most accessible tissue: Callus, score: 77.168 | N | N | N | N |
| vg0522745784 | CATAATGCTATTGCT -> C | LOC_Os05g38770.1 | intron_variant ; MODIFIER | silent_mutation | Average:42.946; most accessible tissue: Callus, score: 77.168 | N | N | N | N |