| Variant ID: vg1120444927 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 20444927 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AAACATTCTTAGCAAACAAGTTGTATATCTTCCTCTCCTGTGCTTCCTAAATCTAAGTTCCTATGGCCTATGGGCTCCTATATCCATAGCATACATATAT[G/A]
GGGTTGGGCCCCTTGACTTCGAGGGCCTAGTGCGATGGCACAGCTCGACCCCCCTCAGGGTCGGACCTGCTCATTTCAGTGAAAACATAGTATATGTAAT
ATTACATATACTATGTTTTCACTGAAATGAGCAGGTCCGACCCTGAGGGGGGTCGAGCTGTGCCATCGCACTAGGCCCTCGAAGTCAAGGGGCCCAACCC[C/T]
ATATATGTATGCTATGGATATAGGAGCCCATAGGCCATAGGAACTTAGATTTAGGAAGCACAGGAGAGGAAGATATACAACTTGTTTGCTAAGAATGTTT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 81.80% | 0.20% | 2.12% | 15.91% | NA |
| All Indica | 2759 | 74.20% | 0.00% | 2.54% | 23.20% | NA |
| All Japonica | 1512 | 96.00% | 0.50% | 1.19% | 2.31% | NA |
| Aus | 269 | 74.00% | 0.00% | 3.72% | 22.30% | NA |
| Indica I | 595 | 54.60% | 0.00% | 2.02% | 43.36% | NA |
| Indica II | 465 | 80.40% | 0.00% | 3.66% | 15.91% | NA |
| Indica III | 913 | 78.30% | 0.00% | 2.96% | 18.73% | NA |
| Indica Intermediate | 786 | 80.70% | 0.10% | 1.78% | 17.43% | NA |
| Temperate Japonica | 767 | 97.40% | 0.00% | 1.69% | 0.91% | NA |
| Tropical Japonica | 504 | 92.50% | 1.40% | 0.60% | 5.56% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 87.50% | 0.00% | 2.08% | 10.42% | NA |
| Intermediate | 90 | 92.20% | 0.00% | 0.00% | 7.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1120444927 | G -> A | LOC_Os11g34880.1 | 3_prime_UTR_variant ; 197.0bp to feature; MODIFIER | silent_mutation | Average:38.9; most accessible tissue: Callus, score: 74.376 | N | N | N | N |
| vg1120444927 | G -> DEL | N | N | silent_mutation | Average:38.9; most accessible tissue: Callus, score: 74.376 | N | N | N | N |