| Variant ID: vg0432301621 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr04 | Position: 32301621 |
| Reference Allele: C | Alternative Allele: CT |
| Primary Allele: C | Secondary Allele: CT |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 123. )
TTTATGTTGGTATTATTAGTTAGGGACAATTAGTTATTGTTTAGATCTTTAATGTTTTTTATGCTCTCCATTCAGTGAATTATGTAGAGCGGCTGTAGCT[C/CT]
TTTTAAGCAAAGGTTGAGAATCTTTCCATTCTCTTAAAAAAATTCCATACCAAATTGAATTGAATTACAGATCTGACTATCATTCAGTAACAAGTGGTAA
TTACCACTTGTTACTGAATGATAGTCAGATCTGTAATTCAATTCAATTTGGTATGGAATTTTTTTAAGAGAATGGAAAGATTCTCAACCTTTGCTTAAAA[G/AG]
AGCTACAGCCGCTCTACATAATTCACTGAATGGAGAGCATAAAAAACATTAAAGATCTAAACAATAACTAATTGTCCCTAACTAATAATACCAACATAAA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of CT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 72.70% | 26.70% | 0.30% | 0.25% | NA |
| All Indica | 2759 | 55.30% | 43.80% | 0.43% | 0.43% | NA |
| All Japonica | 1512 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.37% | 0.00% | NA |
| Indica I | 595 | 26.20% | 72.80% | 0.50% | 0.50% | NA |
| Indica II | 465 | 67.70% | 31.80% | 0.22% | 0.22% | NA |
| Indica III | 913 | 65.10% | 34.00% | 0.33% | 0.66% | NA |
| Indica Intermediate | 786 | 58.70% | 40.50% | 0.64% | 0.25% | NA |
| Temperate Japonica | 767 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 94.60% | 5.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 1.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 77.80% | 22.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0432301621 | C -> CT | LOC_Os04g54240.1 | splice_region_variant ; LOW | silent_mutation | Average:49.603; most accessible tissue: Minghui63 panicle, score: 87.605 | N | N | N | N |
| vg0432301621 | C -> CT | LOC_Os04g54240.1 | 3_prime_UTR_variant ; 472.0bp to feature; MODIFIER | silent_mutation | Average:49.603; most accessible tissue: Minghui63 panicle, score: 87.605 | N | N | N | N |
| vg0432301621 | C -> CT | LOC_Os04g54230.1 | upstream_gene_variant ; 3490.0bp to feature; MODIFIER | silent_mutation | Average:49.603; most accessible tissue: Minghui63 panicle, score: 87.605 | N | N | N | N |
| vg0432301621 | C -> CT | LOC_Os04g54250.1 | downstream_gene_variant ; 3195.0bp to feature; MODIFIER | silent_mutation | Average:49.603; most accessible tissue: Minghui63 panicle, score: 87.605 | N | N | N | N |
| vg0432301621 | C -> DEL | N | N | silent_mutation | Average:49.603; most accessible tissue: Minghui63 panicle, score: 87.605 | N | N | N | N |