| Variant ID: vg1000677169 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr10 | Position: 677169 |
| Reference Allele: C | Alternative Allele: CT |
| Primary Allele: CT | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 345. )
AGATGAAACTGTAGAGATAGTTGCAATCTTCAGATCATCCTGCAGCATGATATGATATACAGTATATGACCCACCCAATTTAAGGCACATACATTCAGTT[C/CT]
TTTTTTTCCAATGGATCACATCTTTGTTGACGATCAGTTCACAAACTAGTCACAATCACATCGTTATTACTTCTGCTTCTTCAAGCATTCATGTAACATC
GATGTTACATGAATGCTTGAAGAAGCAGAAGTAATAACGATGTGATTGTGACTAGTTTGTGAACTGATCGTCAACAAAGATGTGATCCATTGGAAAAAAA[G/AG]
AACTGAATGTATGTGCCTTAAATTGGGTGGGTCATATACTGTATATCATATCATGCTGCAGGATGATCTGAAGATTGCAACTATCTCTACAGTTTCATCT
| Populations | Population Size | Frequency of CT(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 58.80% | 40.90% | 0.21% | 0.00% | NA |
| All Indica | 2759 | 67.30% | 32.50% | 0.18% | 0.00% | NA |
| All Japonica | 1512 | 45.30% | 54.60% | 0.07% | 0.00% | NA |
| Aus | 269 | 34.90% | 65.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 54.60% | 45.40% | 0.00% | 0.00% | NA |
| Indica II | 465 | 80.00% | 19.80% | 0.22% | 0.00% | NA |
| Indica III | 913 | 70.00% | 30.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 66.20% | 33.30% | 0.51% | 0.00% | NA |
| Temperate Japonica | 767 | 12.50% | 87.50% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 92.50% | 7.50% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 51.00% | 48.50% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 90.60% | 9.40% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 65.60% | 30.00% | 4.44% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1000677169 | C -> CT | LOC_Os10g02070.1 | 3_prime_UTR_variant ; 179.0bp to feature; MODIFIER | silent_mutation | Average:64.51; most accessible tissue: Minghui63 root, score: 79.298 | N | N | N | N |
| vg1000677169 | C -> CT | LOC_Os10g02080.1 | downstream_gene_variant ; 2929.0bp to feature; MODIFIER | silent_mutation | Average:64.51; most accessible tissue: Minghui63 root, score: 79.298 | N | N | N | N |