| Variant ID: vg0204059402 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 4059402 |
| Reference Allele: C | Alternative Allele: CA,CAA,CAAA |
| Primary Allele: C | Secondary Allele: CA |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 300. )
TCTTTGCACCTCCATCTGCATTCTGATGGCATCGTTCACGTTGCGGCTGAGAGAGAGAATTTCACACACAAGCAAACACAAAAATGGAGTTAGGAAAGAA[C/CA,CAA,CAAA]
AAAAAAAAAGAGTAACTGAACAAGGACTAAGAAAGAAATTAAAATCTTAAACCGGATTAATTCTACAGTACTAGTGTACTGTTACTAGTGTACTAGTGTA
TACACTAGTACACTAGTAACAGTACACTAGTACTGTAGAATTAATCCGGTTTAAGATTTTAATTTCTTTCTTAGTCCTTGTTCAGTTACTCTTTTTTTTT[G/TG,TTG,TTTG]
TTCTTTCCTAACTCCATTTTTGTGTTTGCTTGTGTGTGAAATTCTCTCTCTCAGCCGCAACGTGAACGATGCCATCAGAATGCAGATGGAGGTGCAAAGA
| 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 | 49.90% | 47.50% | 1.12% | 0.91% | CAA: 0.53%; CAAA: 0.02% |
| All Indica | 2759 | 20.90% | 75.20% | 1.67% | 1.52% | CAA: 0.76% |
| All Japonica | 1512 | 99.50% | 0.40% | 0.07% | 0.00% | NA |
| Aus | 269 | 48.00% | 48.00% | 2.23% | 0.00% | CAA: 1.49%; CAAA: 0.37% |
| Indica I | 595 | 30.10% | 69.40% | 0.50% | 0.00% | NA |
| Indica II | 465 | 14.60% | 83.20% | 0.86% | 1.08% | CAA: 0.22% |
| Indica III | 913 | 18.50% | 73.30% | 3.72% | 2.74% | CAA: 1.75% |
| Indica Intermediate | 786 | 20.40% | 77.00% | 0.64% | 1.53% | CAA: 0.51% |
| Temperate Japonica | 767 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.20% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 93.80% | 6.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 64.40% | 34.40% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0204059402 | C -> DEL | N | N | silent_mutation | Average:41.332; most accessible tissue: Callus, score: 60.214 | N | N | N | N |
| vg0204059402 | C -> CA | LOC_Os02g07770.1 | intron_variant ; MODIFIER | silent_mutation | Average:41.332; most accessible tissue: Callus, score: 60.214 | N | N | N | N |
| vg0204059402 | C -> CAAA | LOC_Os02g07770.1 | intron_variant ; MODIFIER | silent_mutation | Average:41.332; most accessible tissue: Callus, score: 60.214 | N | N | N | N |
| vg0204059402 | C -> CAA | LOC_Os02g07770.1 | intron_variant ; MODIFIER | silent_mutation | Average:41.332; most accessible tissue: Callus, score: 60.214 | N | N | N | N |