| Variant ID: vg1120445123 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 20445123 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GTAATATACATGGATTATTATAAAATCAAACAAATTAAAACCAACACATATCTTGGCCAATTGTTCATCACAACATAATCATCACCATGATTTTACAGTT[C/A]
CTACATGCTCAAGTCAAGTGTGGGGCTGTTGGGATTCATATGGATCTGTCTTCTAATTCCAGCCTCGACAACCTCGTGCATTTCCTCAGGGCAGTTGTTA
TAACAACTGCCCTGAGGAAATGCACGAGGTTGTCGAGGCTGGAATTAGAAGACAGATCCATATGAATCCCAACAGCCCCACACTTGACTTGAGCATGTAG[G/T]
AACTGTAAAATCATGGTGATGATTATGTTGTGATGAACAATTGGCCAAGATATGTGTTGGTTTTAATTTGTTTGATTTTATAATAATCCATGTATATTAC
| 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 | 78.30% | 0.10% | 0.80% | 20.82% | NA |
| All Indica | 2759 | 70.90% | 0.00% | 0.65% | 28.49% | NA |
| All Japonica | 1512 | 95.00% | 0.20% | 1.06% | 3.70% | NA |
| Aus | 269 | 53.20% | 0.00% | 1.49% | 45.35% | NA |
| Indica I | 595 | 53.80% | 0.00% | 0.84% | 45.38% | NA |
| Indica II | 465 | 79.40% | 0.00% | 0.00% | 20.65% | NA |
| Indica III | 913 | 71.60% | 0.00% | 1.42% | 26.94% | NA |
| Indica Intermediate | 786 | 77.90% | 0.00% | 0.00% | 22.14% | NA |
| Temperate Japonica | 767 | 96.60% | 0.00% | 1.96% | 1.43% | NA |
| Tropical Japonica | 504 | 90.50% | 0.60% | 0.20% | 8.73% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 87.50% | 0.00% | 0.00% | 12.50% | NA |
| Intermediate | 90 | 88.90% | 2.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1120445123 | C -> A | LOC_Os11g34880.1 | 3_prime_UTR_variant ; 1.0bp to feature; MODIFIER | silent_mutation | Average:40.033; most accessible tissue: Zhenshan97 young leaf, score: 71.497 | N | N | N | N |
| vg1120445123 | C -> DEL | N | N | silent_mutation | Average:40.033; most accessible tissue: Zhenshan97 young leaf, score: 71.497 | N | N | N | N |