| Variant ID: vg0322195583 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 22195583 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GCTTCCCGGAGGCGGTCCGCGGCTTCTCGCCGGTCAGCTTCCCGCCTCCGGGCCTCCGCTGTCGCCGTCTCCTCGGCCTCAGACCGGCCGGACTTGGAAT[G/A]
GCGGGGGGGGGGCGCGACGGGATCTCGCTGAGGCAGAAGAAAAACCAGAAGACAAAAAGAAACGGGTGAGTGAAAACTCGCCTTGGGAGATGGGAGAATA
TATTCTCCCATCTCCCAAGGCGAGTTTTCACTCACCCGTTTCTTTTTGTCTTCTGGTTTTTCTTCTGCCTCAGCGAGATCCCGTCGCGCCCCCCCCCCGC[C/T]
ATTCCAAGTCCGGCCGGTCTGAGGCCGAGGAGACGGCGACAGCGGAGGCCCGGAGGCGGGAAGCTGACCGGCGAGAAGCCGCGGACCGCCTCCGGGAAGC
| 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 | 4.50% | 0.10% | 24.63% | 70.78% | NA |
| All Indica | 2759 | 2.10% | 0.10% | 25.88% | 71.95% | NA |
| All Japonica | 1512 | 8.70% | 0.20% | 22.29% | 68.78% | NA |
| Aus | 269 | 5.90% | 0.00% | 33.83% | 60.22% | NA |
| Indica I | 595 | 0.50% | 0.00% | 16.47% | 83.03% | NA |
| Indica II | 465 | 1.70% | 0.00% | 6.67% | 91.61% | NA |
| Indica III | 913 | 4.30% | 0.20% | 46.77% | 48.74% | NA |
| Indica Intermediate | 786 | 1.00% | 0.00% | 20.10% | 78.88% | NA |
| Temperate Japonica | 767 | 10.40% | 0.10% | 5.74% | 83.70% | NA |
| Tropical Japonica | 504 | 4.20% | 0.40% | 49.21% | 46.23% | NA |
| Japonica Intermediate | 241 | 12.90% | 0.00% | 18.67% | 68.46% | NA |
| VI/Aromatic | 96 | 2.10% | 0.00% | 5.21% | 92.71% | NA |
| Intermediate | 90 | 4.40% | 0.00% | 18.89% | 76.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0322195583 | G -> A | LOC_Os03g39930.1 | 5_prime_UTR_variant ; 462.0bp to feature; MODIFIER | silent_mutation | Average:20.77; most accessible tissue: Minghui63 panicle, score: 34.226 | N | N | N | N |
| vg0322195583 | G -> A | LOC_Os03g39920.1 | downstream_gene_variant ; 2413.0bp to feature; MODIFIER | silent_mutation | Average:20.77; most accessible tissue: Minghui63 panicle, score: 34.226 | N | N | N | N |
| vg0322195583 | G -> A | LOC_Os03g39940.1 | downstream_gene_variant ; 2312.0bp to feature; MODIFIER | silent_mutation | Average:20.77; most accessible tissue: Minghui63 panicle, score: 34.226 | N | N | N | N |
| vg0322195583 | G -> DEL | N | N | silent_mutation | Average:20.77; most accessible tissue: Minghui63 panicle, score: 34.226 | N | N | N | N |