| Variant ID: vg1105342634 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5342634 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GGTGATTACAAATTTCTAGGTGAGCTCATGAATATGTTGATCAGTGCAGAAGACTACACGGTCAACTGAGCAAAGACTACTAGAAATGCATAATAAAACG[T/C]
CAAACCGCTTCTGGGTAGATGACCTAAGTAACCTAGGGACTGGTTTAGTTCCCAACTTTTTCTTCAAACTTCCAACTTTTCCATCACATGAAAACTTTCC
GGAAAGTTTTCATGTGATGGAAAAGTTGGAAGTTTGAAGAAAAAGTTGGGAACTAAACCAGTCCCTAGGTTACTTAGGTCATCTACCCAGAAGCGGTTTG[A/G]
CGTTTTATTATGCATTTCTAGTAGTCTTTGCTCAGTTGACCGTGTAGTCTTCTGCACTGATCAACATATTCATGAGCTCACCTAGAAATTTGTAATCACC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.70% | 0.10% | 0.17% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 88.50% | 6.20% | 5.21% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 1.10% | 2.22% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105342634 | T -> C | LOC_Os11g09970.1 | 3_prime_UTR_variant ; 292.0bp to feature; MODIFIER | silent_mutation | Average:68.029; most accessible tissue: Zhenshan97 root, score: 78.34 | N | N | N | N |
| vg1105342634 | T -> C | LOC_Os11g09960.1 | upstream_gene_variant ; 2129.0bp to feature; MODIFIER | silent_mutation | Average:68.029; most accessible tissue: Zhenshan97 root, score: 78.34 | N | N | N | N |