| Variant ID: vg0607439520 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 7439520 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 259. )
GTATCAAGCCCATTTCCCTCGATGCACTGTCTATCACATTACGTGGTAGCCCCTTGGTAAACTGATCTGCTAGATTTCTAGCCGTTTGGACATAGTCCAA[T/A]
GCTATCACTCCGGAGTTTTTCTGCTTTCTGACAGATTTCAGTCTTCTCTTGATGTGTCTAGATGACTTCATGTTGTCCTTTGAACTGTTCACTTTAATAA
TTATTAAAGTGAACAGTTCAAAGGACAACATGAAGTCATCTAGACACATCAAGAGAAGACTGAAATCTGTCAGAAAGCAGAAAAACTCCGGAGTGATAGC[A/T]
TTGGACTATGTCCAAACGGCTAGAAATCTAGCAGATCAGTTTACCAAGGGGCTACCACGTAATGTGATAGACAGTGCATCGAGGGAAATGGGCTTGATAC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 0.70% | 0.10% | 3.60% | 95.56% | NA |
| All Indica | 2759 | 0.80% | 0.10% | 0.80% | 98.22% | NA |
| All Japonica | 1512 | 0.60% | 0.10% | 4.17% | 95.17% | NA |
| Aus | 269 | 0.40% | 0.40% | 2.97% | 96.28% | NA |
| Indica I | 595 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Indica II | 465 | 2.40% | 0.00% | 1.51% | 96.13% | NA |
| Indica III | 913 | 0.30% | 0.40% | 0.77% | 98.47% | NA |
| Indica Intermediate | 786 | 1.10% | 0.00% | 1.02% | 97.84% | NA |
| Temperate Japonica | 767 | 0.50% | 0.00% | 5.48% | 94.00% | NA |
| Tropical Japonica | 504 | 0.60% | 0.00% | 2.58% | 96.83% | NA |
| Japonica Intermediate | 241 | 0.80% | 0.40% | 3.32% | 95.44% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 72.92% | 27.08% | NA |
| Intermediate | 90 | 1.10% | 0.00% | 7.78% | 91.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0607439520 | T -> A | LOC_Os06g13500.1 | synonymous_variant ; p.Ala1233Ala; LOW | synonymous_codon | Average:9.154; most accessible tissue: Minghui63 panicle, score: 25.313 | N | N | N | N |
| vg0607439520 | T -> DEL | LOC_Os06g13500.1 | N | frameshift_variant | Average:9.154; most accessible tissue: Minghui63 panicle, score: 25.313 | N | N | N | N |