| Variant ID: vg0334688449 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr03 | Position: 34688449 |
| Reference Allele: CAT | Alternative Allele: C |
| Primary Allele: CAT | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TAACTTTACAAATTACAAATGTTCTTACATAATATAATCAACCTATAGTACAGAACAATCTTTCTAACTTTCATAAGAAAGATTGTTAGACCCAACCCCT[CAT/C]
ATTTTGTATTCACAAAGCATGGCGGCATGGTAGCTTAAAGATGATAAATTAATTACCAACAATAATTAATTCATCTCAAAATCTCAACCTAAGTAGGAAC
GTTCCTACTTAGGTTGAGATTTTGAGATGAATTAATTATTGTTGGTAATTAATTTATCATCTTTAAGCTACCATGCCGCCATGCTTTGTGAATACAAAAT[ATG/G]
AGGGGTTGGGTCTAACAATCTTTCTTATGAAAGTTAGAAAGATTGTTCTGTACTATAGGTTGATTATATTATGTAAGAACATTTGTAATTTGTAAAGTTA
| Populations | Population Size | Frequency of CAT(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.60% | 0.40% | 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 | 98.90% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0334688449 | CAT -> C | LOC_Os03g61060.1 | 3_prime_UTR_variant ; 122.0bp to feature; MODIFIER | N | Average:81.688; most accessible tissue: Callus, score: 95.443 | N | N | N | N |
| vg0334688449 | CAT -> C | LOC_Os03g61060.2 | 3_prime_UTR_variant ; 122.0bp to feature; MODIFIER | N | Average:81.688; most accessible tissue: Callus, score: 95.443 | N | N | N | N |
| vg0334688449 | CAT -> C | LOC_Os03g61050.1 | downstream_gene_variant ; 369.0bp to feature; MODIFIER | N | Average:81.688; most accessible tissue: Callus, score: 95.443 | N | N | N | N |
| vg0334688449 | CAT -> C | LOC_Os03g61070.1 | downstream_gene_variant ; 4458.0bp to feature; MODIFIER | N | Average:81.688; most accessible tissue: Callus, score: 95.443 | N | N | N | N |