| Variant ID: vg0209333915 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 9333915 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CCCAGGAGGCAAGGTACACCAAAAGTTGATACAATTCAGAGTTTAACAAGCGGAAGCGTAAATAGTTATTTATTACATGGGCAGCGACGGCCCAGCACAC[T/A]
CAAAGACAACGAAAAACAGCAGAAGACTAAGGCGACGACCACAGGCGCTTGACGGCAGGCACGAGCTAGACACCAAAGCCTTCATCCTCCAGGGGCTCCT
AGGAGCCCCTGGAGGATGAAGGCTTTGGTGTCTAGCTCGTGCCTGCCGTCAAGCGCCTGTGGTCGTCGCCTTAGTCTTCTGCTGTTTTTCGTTGTCTTTG[A/T]
GTGTGCTGGGCCGTCGCTGCCCATGTAATAAATAACTATTTACGCTTCCGCTTGTTAAACTCTGAATTGTATCAACTTTTGGTGTACCTTGCCTCCTGGG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 51.70% | 0.10% | 2.81% | 45.32% | NA |
| All Indica | 2759 | 27.10% | 0.30% | 4.10% | 68.50% | NA |
| All Japonica | 1512 | 97.30% | 0.00% | 0.13% | 2.58% | NA |
| Aus | 269 | 30.10% | 0.00% | 5.58% | 64.31% | NA |
| Indica I | 595 | 26.20% | 0.00% | 2.52% | 71.26% | NA |
| Indica II | 465 | 30.50% | 0.20% | 4.52% | 64.73% | NA |
| Indica III | 913 | 23.90% | 0.40% | 4.60% | 71.08% | NA |
| Indica Intermediate | 786 | 29.60% | 0.30% | 4.45% | 65.65% | NA |
| Temperate Japonica | 767 | 98.00% | 0.00% | 0.13% | 1.83% | NA |
| Tropical Japonica | 504 | 96.20% | 0.00% | 0.20% | 3.57% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.00% | 0.00% | 2.90% | NA |
| VI/Aromatic | 96 | 87.50% | 0.00% | 1.04% | 11.46% | NA |
| Intermediate | 90 | 65.60% | 0.00% | 2.22% | 32.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0209333915 | T -> A | LOC_Os02g16390.1 | upstream_gene_variant ; 1915.0bp to feature; MODIFIER | silent_mutation | Average:4.363; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0209333915 | T -> A | LOC_Os02g16380.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.363; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0209333915 | T -> DEL | N | N | silent_mutation | Average:4.363; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |