| Variant ID: vg0512046495 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 12046495 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CTGATACCAACTTGTCACGCCCGGAATTTCTATCCAAAATTCCAAACGCTTACATGTGTGTGAACCCTCATCCAGGAATCAGCCGAGGCACACAATAACA[A/G]
ATTGATAATAGAGTACAAATATTACTCTAATTAATAAGCGAATAAAATGTCATTACAGAGGTAGATAGTTCCTCTCAATCAATAAAGATCTAAGCAGCGG
CCGCTGCTTAGATCTTTATTGATTGAGAGGAACTATCTACCTCTGTAATGACATTTTATTCGCTTATTAATTAGAGTAATATTTGTACTCTATTATCAAT[T/C]
TGTTATTGTGTGCCTCGGCTGATTCCTGGATGAGGGTTCACACACATGTAAGCGTTTGGAATTTTGGATAGAAATTCCGGGCGTGACAAGTTGGTATCAG
| 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 | 87.10% | 0.10% | 2.69% | 10.09% | NA |
| All Indica | 2759 | 86.30% | 0.10% | 4.46% | 9.06% | NA |
| All Japonica | 1512 | 99.70% | 0.00% | 0.00% | 0.33% | NA |
| Aus | 269 | 21.60% | 0.00% | 0.00% | 78.44% | NA |
| Indica I | 595 | 91.90% | 0.00% | 7.73% | 0.34% | NA |
| Indica II | 465 | 98.10% | 0.20% | 0.65% | 1.08% | NA |
| Indica III | 913 | 76.70% | 0.00% | 4.49% | 18.84% | NA |
| Indica Intermediate | 786 | 86.40% | 0.40% | 4.20% | 9.03% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.20% | 0.00% | 0.00% | 0.79% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 3.12% | 1.04% | NA |
| Intermediate | 90 | 87.80% | 0.00% | 1.11% | 11.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0512046495 | A -> DEL | N | N | silent_mutation | Average:21.217; most accessible tissue: Zhenshan97 flag leaf, score: 41.874 | N | N | N | N |
| vg0512046495 | A -> G | LOC_Os05g20510.1 | downstream_gene_variant ; 4601.0bp to feature; MODIFIER | silent_mutation | Average:21.217; most accessible tissue: Zhenshan97 flag leaf, score: 41.874 | N | N | N | N |
| vg0512046495 | A -> G | LOC_Os05g20520.1 | intron_variant ; MODIFIER | silent_mutation | Average:21.217; most accessible tissue: Zhenshan97 flag leaf, score: 41.874 | N | N | N | N |