| Variant ID: vg0322193685 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 22193685 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TTGGGACCTGGGCACGAGCCCTCGTTCAAGCCAAGACACAGAAGGACCGCGGCACAGACCATCCTCGTCTCATACACATAACAAACATAACTGACGTAGA[A/G]
ATTTCCTCTTTATTTGATTACAGATTAAATCAGTCTATACAAGAAGGGGGCCCGAAGGCCTCGGAAGAAGAAGGAGAAGTTATTAAGATTGGCGGGGGCC
GGCCCCCGCCAATCTTAATAACTTCTCCTTCTTCTTCCGAGGCCTTCGGGCCCCCTTCTTGTATAGACTGATTTAATCTGTAATCAAATAAAGAGGAAAT[T/C]
TCTACGTCAGTTATGTTTGTTATGTGTATGAGACGAGGATGGTCTGTGCCGCGGTCCTTCTGTGTCTTGGCTTGAACGAGGGCTCGTGCCCAGGTCCCAA
| 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 | 62.40% | 0.10% | 1.27% | 36.16% | NA |
| All Indica | 2759 | 48.00% | 0.30% | 1.12% | 50.60% | NA |
| All Japonica | 1512 | 93.10% | 0.00% | 0.20% | 6.75% | NA |
| Aus | 269 | 48.70% | 0.00% | 8.92% | 42.38% | NA |
| Indica I | 595 | 25.20% | 0.50% | 0.67% | 73.61% | NA |
| Indica II | 465 | 35.10% | 0.00% | 2.15% | 62.80% | NA |
| Indica III | 913 | 74.40% | 0.20% | 0.99% | 24.42% | NA |
| Indica Intermediate | 786 | 42.40% | 0.30% | 1.02% | 56.36% | NA |
| Temperate Japonica | 767 | 98.60% | 0.00% | 0.00% | 1.43% | NA |
| Tropical Japonica | 504 | 94.60% | 0.00% | 0.60% | 4.76% | NA |
| Japonica Intermediate | 241 | 72.20% | 0.00% | 0.00% | 27.80% | NA |
| VI/Aromatic | 96 | 29.20% | 0.00% | 1.04% | 69.79% | NA |
| Intermediate | 90 | 65.60% | 0.00% | 1.11% | 33.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0322193685 | A -> DEL | N | N | silent_mutation | Average:12.508; most accessible tissue: Zhenshan97 panicle, score: 32.308 | N | N | N | N |
| vg0322193685 | A -> G | LOC_Os03g39930.1 | 3_prime_UTR_variant ; 108.0bp to feature; MODIFIER | silent_mutation | Average:12.508; most accessible tissue: Zhenshan97 panicle, score: 32.308 | N | N | N | N |
| vg0322193685 | A -> G | LOC_Os03g39920.1 | downstream_gene_variant ; 515.0bp to feature; MODIFIER | silent_mutation | Average:12.508; most accessible tissue: Zhenshan97 panicle, score: 32.308 | N | N | N | N |
| vg0322193685 | A -> G | LOC_Os03g39940.1 | downstream_gene_variant ; 4210.0bp to feature; MODIFIER | silent_mutation | Average:12.508; most accessible tissue: Zhenshan97 panicle, score: 32.308 | N | N | N | N |