| Variant ID: vg0203136261 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 3136261 |
| Reference Allele: AC | Alternative Allele: A |
| Primary Allele: AC | Secondary Allele: A |
Inferred Ancestral Allele : AC (evidence from allele frequency in Oryza rufipogon: AC: 0.76, A: 0.23, others allele: 0.00, population size: 209. )
ATGTATTCCTTCCAGTTTATTATCAAAAAAACGAGTTCCCTCCAATGTCCTTTTCTTTATTTTTGTATTTTCCGCCTTTCATAGGAAAACCTGAACCAGA[AC/A]
AAGAGGTATATTTCGTGCACAACTAGACTAAGCTTGTAACCGGACATGCTGCTTGGATCTTAACAGCAGCTCAAACTGACCAAAGTTATCACAAAAAGTA
TACTTTTTGTGATAACTTTGGTCAGTTTGAGCTGCTGTTAAGATCCAAGCAGCATGTCCGGTTACAAGCTTAGTCTAGTTGTGCACGAAATATACCTCTT[GT/T]
TCTGGTTCAGGTTTTCCTATGAAAGGCGGAAAATACAAAAATAAAGAAAAGGACATTGGAGGGAACTCGTTTTTTTGATAATAAACTGGAAGGAATACAT
| Populations | Population Size | Frequency of AC(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 55.10% | 42.60% | 0.00% | 2.33% | NA |
| All Indica | 2759 | 38.50% | 59.00% | 0.00% | 2.54% | NA |
| All Japonica | 1512 | 90.70% | 9.10% | 0.00% | 0.20% | NA |
| Aus | 269 | 17.10% | 82.50% | 0.00% | 0.37% | NA |
| Indica I | 595 | 53.60% | 46.40% | 0.00% | 0.00% | NA |
| Indica II | 465 | 53.50% | 46.20% | 0.00% | 0.22% | NA |
| Indica III | 913 | 18.00% | 77.80% | 0.00% | 4.27% | NA |
| Indica Intermediate | 786 | 42.00% | 54.20% | 0.00% | 3.82% | NA |
| Temperate Japonica | 767 | 84.50% | 15.50% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 98.60% | 1.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 93.80% | 5.00% | 0.00% | 1.24% | NA |
| VI/Aromatic | 96 | 64.60% | 4.20% | 0.00% | 31.25% | NA |
| Intermediate | 90 | 68.90% | 24.40% | 0.00% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0203136261 | AC -> A | LOC_Os02g06270.1 | upstream_gene_variant ; 1277.0bp to feature; MODIFIER | silent_mutation | Average:53.021; most accessible tissue: Callus, score: 82.944 | N | N | N | N |
| vg0203136261 | AC -> A | LOC_Os02g06280.1 | intron_variant ; MODIFIER | silent_mutation | Average:53.021; most accessible tissue: Callus, score: 82.944 | N | N | N | N |
| vg0203136261 | AC -> DEL | N | N | silent_mutation | Average:53.021; most accessible tissue: Callus, score: 82.944 | N | N | N | N |