| Variant ID: vg0200790780 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 790780 |
| Reference Allele: CAAGCTAAGCTTGAACTAACCCA | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: CAAGCTAAGCTTGAACTAAC CCA |
Inferred Ancestral Allele: Not determined.
GCTAGACTCTATGTACTGTAATGCTTTTGTTATTATTTTGGAAAAAAAAGGGTGAGAATTCTTCCTTGGCTGGAATTTCAACTGGCCTAAGAATTGTGAT[CAAGCTAAGCTTGAACTAACCCA/C]
AAGCTAAGTACTCTCTGTAACTGCTAATTACCAATTAGAGAGGGGACTAGACTAGGCTAGAATTCACAATTGTGAAGAGGGATGCATTGGTGAATGCAGC
GCTGCATTCACCAATGCATCCCTCTTCACAATTGTGAATTCTAGCCTAGTCTAGTCCCCTCTCTAATTGGTAATTAGCAGTTACAGAGAGTACTTAGCTT[TGGGTTAGTTCAAGCTTAGCTTG/G]
ATCACAATTCTTAGGCCAGTTGAAATTCCAGCCAAGGAAGAATTCTCACCCTTTTTTTTCCAAAATAATAACAAAAGCATTACAGTACATAGAGTCTAGC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of CAAGCTAAGCTTGAACTAAC CCA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 52.80% | 47.00% | 0.19% | 0.00% | NA |
| All Indica | 2759 | 86.30% | 13.40% | 0.29% | 0.00% | NA |
| All Japonica | 1512 | 5.30% | 94.60% | 0.07% | 0.00% | NA |
| Aus | 269 | 3.30% | 96.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.20% | 1.80% | 0.00% | 0.00% | NA |
| Indica II | 465 | 69.00% | 29.90% | 1.08% | 0.00% | NA |
| Indica III | 913 | 88.90% | 11.00% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 84.60% | 15.10% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 0.50% | 99.50% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 9.50% | 90.30% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 11.60% | 88.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 1.00% | 99.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 24.40% | 75.60% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0200790780 | CAAGCTAAGCTTGAACTAACCCA -> C | LOC_Os02g02360.1 | downstream_gene_variant ; 1546.0bp to feature; MODIFIER | silent_mutation | Average:61.379; most accessible tissue: Callus, score: 86.638 | N | N | N | N |
| vg0200790780 | CAAGCTAAGCTTGAACTAACCCA -> C | LOC_Os02g02380.1 | downstream_gene_variant ; 4285.0bp to feature; MODIFIER | silent_mutation | Average:61.379; most accessible tissue: Callus, score: 86.638 | N | N | N | N |
| vg0200790780 | CAAGCTAAGCTTGAACTAACCCA -> C | LOC_Os02g02370.1 | intron_variant ; MODIFIER | silent_mutation | Average:61.379; most accessible tissue: Callus, score: 86.638 | N | N | N | N |