| Variant ID: vg1101256004 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 1256004 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 241. )
TGGCTTGTCCAGGAGCATTTTTATAGCAAAGATTTTATTGTAAGTGATGATGTCCCCTCTCTTTCCAGTATGTTCTATGCATTTTACTTGACTTATATTT[G/A]
CCCAAAATGAGTCCGTTTGTTAACTAAATACAGGCAATGAGCCTTAGAAACTCTCGGAACAGAGCAGGCTTAAAAATGCCTCATCGCACTGGAAGCAAAC
GTTTGCTTCCAGTGCGATGAGGCATTTTTAAGCCTGCTCTGTTCCGAGAGTTTCTAAGGCTCATTGCCTGTATTTAGTTAACAAACGGACTCATTTTGGG[C/T]
AAATATAAGTCAAGTAAAATGCATAGAACATACTGGAAAGAGAGGGGACATCATCACTTACAATAAAATCTTTGCTATAAAAATGCTCCTGGACAAGCCA
| 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 | 67.70% | 1.00% | 3.30% | 28.02% | NA |
| All Indica | 2759 | 50.70% | 1.40% | 4.64% | 43.24% | NA |
| All Japonica | 1512 | 97.90% | 0.00% | 0.07% | 1.98% | NA |
| Aus | 269 | 71.70% | 2.20% | 8.92% | 17.10% | NA |
| Indica I | 595 | 20.70% | 0.00% | 6.22% | 73.11% | NA |
| Indica II | 465 | 45.60% | 3.20% | 7.31% | 43.87% | NA |
| Indica III | 913 | 68.80% | 1.50% | 3.18% | 26.51% | NA |
| Indica Intermediate | 786 | 55.30% | 1.40% | 3.56% | 39.69% | NA |
| Temperate Japonica | 767 | 98.60% | 0.00% | 0.13% | 1.30% | NA |
| Tropical Japonica | 504 | 97.80% | 0.00% | 0.00% | 2.18% | NA |
| Japonica Intermediate | 241 | 96.30% | 0.00% | 0.00% | 3.73% | NA |
| VI/Aromatic | 96 | 65.60% | 0.00% | 0.00% | 34.38% | NA |
| Intermediate | 90 | 71.10% | 1.10% | 3.33% | 24.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1101256004 | G -> A | LOC_Os11g03330.1 | downstream_gene_variant ; 2024.0bp to feature; MODIFIER | silent_mutation | Average:5.151; most accessible tissue: Minghui63 young leaf, score: 8.301 | N | N | N | N |
| vg1101256004 | G -> A | LOC_Os11g03340.1 | intron_variant ; MODIFIER | silent_mutation | Average:5.151; most accessible tissue: Minghui63 young leaf, score: 8.301 | N | N | N | N |
| vg1101256004 | G -> DEL | N | N | silent_mutation | Average:5.151; most accessible tissue: Minghui63 young leaf, score: 8.301 | N | N | N | N |