| Variant ID: vg1007912254 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7912254 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 390. )
GTACACGGATGGAGGTGGATGAAGTCGGGGGTCGATGGACATTCTCCAGGGCAAATGAAGGCTACACGGGCTGCGGTTCGGTAGTCGAGATGTCATGGCA[C/T]
AGGGCCGGTGTCCTGCTGCTAGGGGCTCAGTCCTGCCTGCCTGTCCCGGGGGTTCCGGCCGTAGGTGGGATTGGGTCGGTACTCTTGTCTATGGCCAGGA
TCCTGGCCATAGACAAGAGTACCGACCCAATCCCACCTACGGCCGGAACCCCCGGGACAGGCAGGCAGGACTGAGCCCCTAGCAGCAGGACACCGGCCCT[G/A]
TGCCATGACATCTCGACTACCGAACCGCAGCCCGTGTAGCCTTCATTTGCCCTGGAGAATGTCCATCGACCCCCGACTTCATCCACCTCCATCCGTGTAC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.10% | 0.00% | 0.00% | 0.89% | NA |
| All Indica | 2759 | 99.90% | 0.10% | 0.00% | 0.04% | NA |
| All Japonica | 1512 | 97.50% | 0.00% | 0.00% | 2.51% | 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 | 99.90% | 0.00% | 0.00% | 0.11% | NA |
| Indica Intermediate | 786 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 98.80% | 0.00% | 0.00% | 1.17% | NA |
| Tropical Japonica | 504 | 95.20% | 0.00% | 0.00% | 4.76% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.00% | 0.00% | 2.07% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 97.80% | 0.00% | 0.00% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1007912254 | C -> T | LOC_Os10g15100.1 | synonymous_variant ; p.His4His; LOW | synonymous_codon | Average:12.485; most accessible tissue: Zhenshan97 flag leaf, score: 23.298 | N | N | N | N |
| vg1007912254 | C -> DEL | LOC_Os10g15100.1 | N | frameshift_variant | Average:12.485; most accessible tissue: Zhenshan97 flag leaf, score: 23.298 | N | N | N | N |