| Variant ID: vg0234310701 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 34310701 |
| Reference Allele: C | Alternative Allele: CA |
| Primary Allele: C | Secondary Allele: CA |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 327. )
GAAGTGTAGCATTCTTCCACAGAGAGGTTTACCAACAGCAGTTGCAACCTTTATAGCCTCTAATGCTTGAAGGCAGCCGATTACTCCTGGAACTAACAAA[C/CA]
AAAAATGTAGACATTGGATCATTCATATAGACAATATGGATGGGATATTAGAAAACCGGCCTCTACATCCACGACAAGTACATTTACATGTACCTATGAA
TTCATAGGTACATGTAAATGTACTTGTCGTGGATGTAGAGGCCGGTTTTCTAATATCCCATCCATATTGTCTATATGAATGATCCAATGTCTACATTTTT[G/TG]
TTTGTTAGTTCCAGGAGTAATCGGCTGCCTTCAAGCATTAGAGGCTATAAAGGTTGCAACTGCTGTTGGTAAACCTCTCTGTGGAAGAATGCTACACTTC
| 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 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0234310701 | C -> CA | LOC_Os02g56040.1 | upstream_gene_variant ; 2973.0bp to feature; MODIFIER | N | Average:45.285; most accessible tissue: Callus, score: 83.15 | N | N | N | N |
| vg0234310701 | C -> CA | LOC_Os02g56060.1 | upstream_gene_variant ; 2004.0bp to feature; MODIFIER | N | Average:45.285; most accessible tissue: Callus, score: 83.15 | N | N | N | N |
| vg0234310701 | C -> CA | LOC_Os02g56050.1 | intron_variant ; MODIFIER | N | Average:45.285; most accessible tissue: Callus, score: 83.15 | N | N | N | N |