| Variant ID: vg1117779681 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 17779681 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, C: 0.01, others allele: 0.00, population size: 112. )
AGTCCAAACCAGTCCCTCAGCTTGGAGAGCAACCAAACCAGGAGATCGAGCCGTTGGTGACCGGTAAAGAAATGACGATAGAACAATTTATTACTGACAC[T/C]
GGTCTAACTACGGATCAATTGCTAGGAGTCGCACCAATCGAAAAGGCGGAAGTGAAATACATGTACGAACTCGGTAAACCGCTTGTCAAGCCTGAGCTGC
GCAGCTCAGGCTTGACAAGCGGTTTACCGAGTTCGTACATGTATTTCACTTCCGCCTTTTCGATTGGTGCGACTCCTAGCAATTGATCCGTAGTTAGACC[A/G]
GTGTCAGTAATAAATTGTTCTATCGTCATTTCTTTACCGGTCACCAACGGCTCGATCTCCTGGTTTGGTTGCTCTCCAAGCTGAGGGACTGGTTTGGACT
| 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 | 17.30% | 6.50% | 2.84% | 73.36% | NA |
| All Indica | 2759 | 7.10% | 1.30% | 1.56% | 89.96% | NA |
| All Japonica | 1512 | 32.30% | 17.60% | 5.42% | 44.71% | NA |
| Aus | 269 | 8.20% | 0.40% | 2.23% | 89.22% | NA |
| Indica I | 595 | 4.50% | 0.80% | 1.68% | 92.94% | NA |
| Indica II | 465 | 20.90% | 0.90% | 1.94% | 76.34% | NA |
| Indica III | 913 | 2.10% | 2.40% | 1.20% | 94.30% | NA |
| Indica Intermediate | 786 | 6.90% | 0.80% | 1.65% | 90.71% | NA |
| Temperate Japonica | 767 | 26.20% | 29.60% | 9.39% | 34.81% | NA |
| Tropical Japonica | 504 | 25.80% | 1.20% | 0.99% | 72.02% | NA |
| Japonica Intermediate | 241 | 65.10% | 13.70% | 2.07% | 19.09% | NA |
| VI/Aromatic | 96 | 90.60% | 0.00% | 1.04% | 8.33% | NA |
| Intermediate | 90 | 26.70% | 3.30% | 2.22% | 67.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1117779681 | T -> DEL | LOC_Os11g30552.1 | N | frameshift_variant | Average:6.294; most accessible tissue: Zhenshan97 flag leaf, score: 12.605 | N | N | N | N |
| vg1117779681 | T -> C | LOC_Os11g30552.1 | synonymous_variant ; p.Thr853Thr; LOW | synonymous_codon | Average:6.294; most accessible tissue: Zhenshan97 flag leaf, score: 12.605 | N | N | N | N |