| Variant ID: vg0323734923 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr03 | Position: 23734923 |
| Reference Allele: CATATTGAGGATT | Alternative Allele: C |
| Primary Allele: CATATTGAGGATT | Secondary Allele: C |
Inferred Ancestral Allele : CATATTGAGGATT (evidence from allele frequency in Oryza rufipogon: CATATTGAGGATT: 1.00, C: 0.01, others allele: 0.00, population size: 263. )
CATGGGACCTCCCCAGTAAGTCTCTAGCTAACTCTTCGATTTCGATCCCCAGTAAGTGTGTTTAGCTTTAAAAACGAGTTTTGAAGGGAGAAATTGTGAG[CATATTGAGGATT/C]
GAACACGGAACATTCGCGGGTTGAAATTGAAGTGCATCTCTAAATTGTGTTTAGCTTTGATTCAGCGAGTAATATAATATGCATGAATATGTCGTCCATT
AATGGACGACATATTCATGCATATTATATTACTCGCTGAATCAAAGCTAAACACAATTTAGAGATGCACTTCAATTTCAACCCGCGAATGTTCCGTGTTC[AATCCTCAATATG/G]
CTCACAATTTCTCCCTTCAAAACTCGTTTTTAAAGCTAAACACACTTACTGGGGATCGAAATCGAAGAGTTAGCTAGAGACTTACTGGGGAGGTCCCATG
| Populations | Population Size | Frequency of CATATTGAGGATT(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 73.20% | 26.20% | 0.17% | 0.47% | NA |
| All Indica | 2759 | 54.90% | 44.00% | 0.29% | 0.72% | NA |
| All Japonica | 1512 | 99.70% | 0.20% | 0.00% | 0.07% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 25.70% | 72.90% | 0.50% | 0.84% | NA |
| Indica II | 465 | 87.70% | 11.60% | 0.43% | 0.22% | NA |
| Indica III | 913 | 54.30% | 45.20% | 0.00% | 0.44% | NA |
| Indica Intermediate | 786 | 58.40% | 39.90% | 0.38% | 1.27% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.40% | 0.40% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 80.00% | 18.90% | 0.00% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0323734923 | CATATTGAGGATT -> C | LOC_Os03g42650.1 | upstream_gene_variant ; 3961.0bp to feature; MODIFIER | silent_mutation | Average:75.149; most accessible tissue: Zhenshan97 root, score: 89.064 | N | N | N | N |
| vg0323734923 | CATATTGAGGATT -> C | LOC_Os03g42650.2 | upstream_gene_variant ; 3961.0bp to feature; MODIFIER | silent_mutation | Average:75.149; most accessible tissue: Zhenshan97 root, score: 89.064 | N | N | N | N |
| vg0323734923 | CATATTGAGGATT -> C | LOC_Os03g42630.1 | intron_variant ; MODIFIER | silent_mutation | Average:75.149; most accessible tissue: Zhenshan97 root, score: 89.064 | N | N | N | N |
| vg0323734923 | CATATTGAGGATT -> DEL | N | N | silent_mutation | Average:75.149; most accessible tissue: Zhenshan97 root, score: 89.064 | N | N | N | N |