Variant ID: vg0318608296 (JBrowse) | Variation Type: SNP |
Chromosome: chr03 | Position: 18608296 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CCAGCCTCTGCCCACACAGAAACGCAAGGGAGAGAAAAACAACACACACACACACACACACACTGTTAAATAAACCGACAGCAAATTGGGGGGGCAACAC[G/A]
AAATCGGGCGCGCCACCCACCCACCCACCTTCCTCCTCGTCGCTGCGCCCCTGGACGATCTGCGCCTTCACCTCCTCGAACAGCAGCGGCTCGAACACAG
CTGTGTTCGAGCCGCTGCTGTTCGAGGAGGTGAAGGCGCAGATCGTCCAGGGGCGCAGCGACGAGGAGGAAGGTGGGTGGGTGGGTGGCGCGCCCGATTT[C/T]
GTGTTGCCCCCCCAATTTGCTGTCGGTTTATTTAACAGTGTGTGTGTGTGTGTGTGTGTTGTTTTTCTCTCCCTTGCGTTTCTGTGTGGGCAGAGGCTGG
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 | 84.70% | 3.70% | 10.98% | 0.61% | NA |
All Indica | 2759 | 75.10% | 6.30% | 18.16% | 0.36% | NA |
All Japonica | 1512 | 97.90% | 0.00% | 0.93% | 1.19% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 72.80% | 3.20% | 24.03% | 0.00% | NA |
Indica II | 465 | 47.50% | 13.10% | 37.85% | 1.51% | NA |
Indica III | 913 | 91.50% | 4.80% | 3.72% | 0.00% | NA |
Indica Intermediate | 786 | 74.30% | 6.50% | 18.83% | 0.38% | NA |
Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 94.20% | 0.00% | 2.18% | 3.57% | NA |
Japonica Intermediate | 241 | 98.80% | 0.00% | 1.24% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 93.30% | 1.10% | 4.44% | 1.11% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0318608296 | G -> A | LOC_Os03g32540.1 | upstream_gene_variant ; 2897.0bp to feature; MODIFIER | silent_mutation | Average:22.237; most accessible tissue: Zhenshan97 panicle, score: 43.098 | N | N | N | N |
vg0318608296 | G -> A | LOC_Os03g32526.1 | intron_variant ; MODIFIER | silent_mutation | Average:22.237; most accessible tissue: Zhenshan97 panicle, score: 43.098 | N | N | N | N |
vg0318608296 | G -> DEL | N | N | silent_mutation | Average:22.237; most accessible tissue: Zhenshan97 panicle, score: 43.098 | N | N | N | N |