| Variant ID: vg1120445117 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 20445117 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GTATATGTAATATACATGGATTATTATAAAATCAAACAAATTAAAACCAACACATATCTTGGCCAATTGTTCATCACAACATAATCATCACCATGATTTT[A/G]
CAGTTCCTACATGCTCAAGTCAAGTGTGGGGCTGTTGGGATTCATATGGATCTGTCTTCTAATTCCAGCCTCGACAACCTCGTGCATTTCCTCAGGGCAG
CTGCCCTGAGGAAATGCACGAGGTTGTCGAGGCTGGAATTAGAAGACAGATCCATATGAATCCCAACAGCCCCACACTTGACTTGAGCATGTAGGAACTG[T/C]
AAAATCATGGTGATGATTATGTTGTGATGAACAATTGGCCAAGATATGTGTTGGTTTTAATTTGTTTGATTTTATAATAATCCATGTATATTACATATAC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 78.30% | 0.20% | 1.21% | 20.27% | NA |
| All Indica | 2759 | 71.00% | 0.00% | 1.09% | 27.91% | NA |
| All Japonica | 1512 | 94.60% | 0.70% | 1.26% | 3.44% | NA |
| Aus | 269 | 53.90% | 0.00% | 2.97% | 43.12% | NA |
| Indica I | 595 | 54.50% | 0.00% | 0.84% | 44.71% | NA |
| Indica II | 465 | 79.10% | 0.00% | 1.08% | 19.78% | NA |
| Indica III | 913 | 71.50% | 0.00% | 1.42% | 27.05% | NA |
| Indica Intermediate | 786 | 78.10% | 0.00% | 0.89% | 20.99% | NA |
| Temperate Japonica | 767 | 96.90% | 0.00% | 2.09% | 1.04% | NA |
| Tropical Japonica | 504 | 89.10% | 2.00% | 0.60% | 8.33% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 87.50% | 0.00% | 0.00% | 12.50% | NA |
| Intermediate | 90 | 91.10% | 0.00% | 0.00% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1120445117 | A -> DEL | N | N | silent_mutation | Average:40.329; most accessible tissue: Zhenshan97 young leaf, score: 72.34 | N | N | N | N |
| vg1120445117 | A -> G | LOC_Os11g34880.1 | 3_prime_UTR_variant ; 7.0bp to feature; MODIFIER | silent_mutation | Average:40.329; most accessible tissue: Zhenshan97 young leaf, score: 72.34 | N | N | N | N |