| Variant ID: vg1013502769 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr10 | Position: 13502769 |
| Reference Allele: G | Alternative Allele: A,GCGC |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 368. )
TCCCCATTTCTAATGCTCCGAGCTGCGAACAAGCAGTTAGAAGATTGACCATTGTGATCTCATCAGGCACCACACTTGCTTCCTGCATCTCATGAAACAA[G/A,GCGC]
GAAAGGGCCTCCTTGCACTGCTTACACTGCACATAACCGGTCATGAGTGCATTCCATGGGAACACATCCCTTTCAGGCATCTCATCAAACACTTTACGTG
CACGTAAAGTGTTTGATGAGATGCCTGAAAGGGATGTGTTCCCATGGAATGCACTCATGACCGGTTATGTGCAGTGTAAGCAGTGCAAGGAGGCCCTTTC[C/T,GCGC]
TTGTTTCATGAGATGCAGGAAGCAAGTGTGGTGCCTGATGAGATCACAATGGTCAATCTTCTAACTGCTTGTTCGCAGCTCGGAGCATTAGAAATGGGGA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.50% | 0.50% | 0.04% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 98.50% | 1.30% | 0.13% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 95.80% | 3.80% | 0.40% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 2.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1013502769 | G -> GCGC | LOC_Os10g26070.1 | disruptive_inframe_insertion ; p.Ser346_Leu347insArg; MODERATE | N | Average:73.121; most accessible tissue: Minghui63 flag leaf, score: 81.811 | N | N | N | N |
| vg1013502769 | G -> GCGC | LOC_Os10g26060.1 | upstream_gene_variant ; 3335.0bp to feature; MODIFIER | N | Average:73.121; most accessible tissue: Minghui63 flag leaf, score: 81.811 | N | N | N | N |
| vg1013502769 | G -> A | LOC_Os10g26070.1 | synonymous_variant ; p.Ser346Ser; LOW | synonymous_codon | Average:73.121; most accessible tissue: Minghui63 flag leaf, score: 81.811 | N | N | N | N |