| Variant ID: vg1200761652 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr12 | Position: 761652 |
| Reference Allele: T | Alternative Allele: TC |
| Primary Allele: T | Secondary Allele: TC |
Inferred Ancestral Allele: Not determined.
AAGTAATAATATTTACAATACCAGCATAGTTTCATTAAATCTATAATTGAATAATTTTTCATAATATACTTGTCTTGGGTTAAAAATGTTACTACTTTTT[T/TC]
TCTACAAAATCAGTCAAACTTATAATAGTTCGACTTTGACTAAAGTCAAAACGTCTTATAACCTGAAACGGAGTAATAGTTAATAAAAACTTTTACAAGT
ACTTGTAAAAGTTTTTATTAACTATTACTCCGTTTCAGGTTATAAGACGTTTTGACTTTAGTCAAAGTCGAACTATTATAAGTTTGACTGATTTTGTAGA[A/GA]
AAAAAGTAGTAACATTTTTAACCCAAGACAAGTATATTATGAAAAATTATTCAATTATAGATTTAATGAAACTATGCTGGTATTGTAAATATTATTACTT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of TC(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.30% | 0.40% | 0.23% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 89.20% | 6.70% | 4.09% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.70% | 0.30% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1200761652 | T -> TC | LOC_Os12g02350.1 | upstream_gene_variant ; 2138.0bp to feature; MODIFIER | silent_mutation | Average:32.535; most accessible tissue: Zhenshan97 flower, score: 78.5 | N | N | N | N |
| vg1200761652 | T -> TC | LOC_Os12g02370.2 | downstream_gene_variant ; 4781.0bp to feature; MODIFIER | silent_mutation | Average:32.535; most accessible tissue: Zhenshan97 flower, score: 78.5 | N | N | N | N |
| vg1200761652 | T -> TC | LOC_Os12g02370.4 | downstream_gene_variant ; 4781.0bp to feature; MODIFIER | silent_mutation | Average:32.535; most accessible tissue: Zhenshan97 flower, score: 78.5 | N | N | N | N |
| vg1200761652 | T -> TC | LOC_Os12g02340.1 | intron_variant ; MODIFIER | silent_mutation | Average:32.535; most accessible tissue: Zhenshan97 flower, score: 78.5 | N | N | N | N |
| vg1200761652 | T -> TC | LOC_Os12g02340.2 | intron_variant ; MODIFIER | silent_mutation | Average:32.535; most accessible tissue: Zhenshan97 flower, score: 78.5 | N | N | N | N |