| Variant ID: vg0409586309 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr04 | Position: 9586309 |
| Reference Allele: TA | Alternative Allele: T |
| Primary Allele: TA | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CGCCTTAGCGATCGATACACCTCTCCGTGGGTTGCTGATCTTGCCGGTGCAGATCAACCCTATTCCTGCATGCAAATCGAAGAAACAAGCAAGAACAAGA[TA/T]
AAAGCAATCTGATATTGCAAATAGGAATTTAATACAAATGATAAGTTGGGGTTCCGAAGAACAAGCAGACGGACGGTCTAGCCGACACGCGCGCTGCAAG
CTTGCAGCGCGCGTGTCGGCTAGACCGTCCGTCTGCTTGTTCTTCGGAACCCCAACTTATCATTTGTATTAAATTCCTATTTGCAATATCAGATTGCTTT[TA/A]
TCTTGTTCTTGCTTGTTTCTTCGATTTGCATGCAGGAATAGGGTTGATCTGCACCGGCAAGATCAGCAACCCACGGAGAGGTGTATCGATCGCTAAGGCG
| Populations | Population Size | Frequency of TA(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 26.80% | 0.40% | 22.92% | 49.85% | NA |
| All Indica | 2759 | 9.90% | 0.80% | 24.76% | 64.55% | NA |
| All Japonica | 1512 | 58.70% | 0.00% | 15.21% | 26.06% | NA |
| Aus | 269 | 13.80% | 0.00% | 39.78% | 46.47% | NA |
| Indica I | 595 | 12.10% | 0.80% | 20.17% | 66.89% | NA |
| Indica II | 465 | 6.20% | 0.60% | 15.70% | 77.42% | NA |
| Indica III | 913 | 11.30% | 0.90% | 26.18% | 61.66% | NA |
| Indica Intermediate | 786 | 8.90% | 0.60% | 31.93% | 58.52% | NA |
| Temperate Japonica | 767 | 83.30% | 0.00% | 12.26% | 4.43% | NA |
| Tropical Japonica | 504 | 16.10% | 0.00% | 21.63% | 62.30% | NA |
| Japonica Intermediate | 241 | 69.70% | 0.00% | 11.20% | 19.09% | NA |
| VI/Aromatic | 96 | 40.60% | 0.00% | 36.46% | 22.92% | NA |
| Intermediate | 90 | 31.10% | 0.00% | 31.11% | 37.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409586309 | TA -> DEL | N | N | silent_mutation | Average:4.859; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0409586309 | TA -> T | LOC_Os04g17510.1 | upstream_gene_variant ; 1619.0bp to feature; MODIFIER | silent_mutation | Average:4.859; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0409586309 | TA -> T | LOC_Os04g17530.1 | downstream_gene_variant ; 1928.0bp to feature; MODIFIER | silent_mutation | Average:4.859; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0409586309 | TA -> T | LOC_Os04g17540.1 | downstream_gene_variant ; 4387.0bp to feature; MODIFIER | silent_mutation | Average:4.859; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0409586309 | TA -> T | LOC_Os04g17520.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.859; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |