| Variant ID: vg1105342599 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5342599 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ATTCAAGAGTAAATTTGTTCGGTCCCTCAGCCTCTGGTGATTACAAATTTCTAGGTGAGCTCATGAATATGTTGATCAGTGCAGAAGACTACACGGTCAA[C/A]
TGAGCAAAGACTACTAGAAATGCATAATAAAACGTCAAACCGCTTCTGGGTAGATGACCTAAGTAACCTAGGGACTGGTTTAGTTCCCAACTTTTTCTTC
GAAGAAAAAGTTGGGAACTAAACCAGTCCCTAGGTTACTTAGGTCATCTACCCAGAAGCGGTTTGACGTTTTATTATGCATTTCTAGTAGTCTTTGCTCA[G/T]
TTGACCGTGTAGTCTTCTGCACTGATCAACATATTCATGAGCTCACCTAGAAATTTGTAATCACCAGAGGCTGAGGGACCGAACAAATTTACTCTTGAAT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1105342599 | C -> A | LOC_Os11g09970.1 | 3_prime_UTR_variant ; 327.0bp to feature; MODIFIER | silent_mutation | Average:66.747; most accessible tissue: Zhenshan97 root, score: 77.733 | N | N | N | N |
| vg1105342599 | C -> A | LOC_Os11g09960.1 | upstream_gene_variant ; 2094.0bp to feature; MODIFIER | silent_mutation | Average:66.747; most accessible tissue: Zhenshan97 root, score: 77.733 | N | N | N | N |