| Variant ID: vg0100790779 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 790779 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GGATTTTTACCTAAAGGAAGACCTTGATGAAAACTGTAATCGTCTTGGAAAAGTTCTAATAACTAGTACGAAAAAATGAACCAAACCAGTGGAAGGACAT[G/A]
CCAAATTGGACCTTCCTCAATAAATAAATAAATAAACCAAACTTTCTCTCCATCTCCAGGTTTTTAGTTATCTTGACTTGCGTATTTTAGAGCACTGGAA
TTCCAGTGCTCTAAAATACGCAAGTCAAGATAACTAAAAACCTGGAGATGGAGAGAAAGTTTGGTTTATTTATTTATTTATTGAGGAAGGTCCAATTTGG[C/T]
ATGTCCTTCCACTGGTTTGGTTCATTTTTTCGTACTAGTTATTAGAACTTTTCCAAGACGATTACAGTTTTCATCAAGGTCTTCCTTTAGGTAAAAATCC
| 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 | 54.40% | 2.10% | 1.40% | 42.02% | NA |
| All Indica | 2759 | 49.20% | 0.80% | 1.88% | 48.06% | NA |
| All Japonica | 1512 | 73.70% | 0.00% | 0.60% | 25.66% | NA |
| Aus | 269 | 9.30% | 29.00% | 0.74% | 60.97% | NA |
| Indica I | 595 | 69.60% | 0.00% | 0.67% | 29.75% | NA |
| Indica II | 465 | 75.70% | 0.20% | 0.65% | 23.44% | NA |
| Indica III | 913 | 17.10% | 1.20% | 2.08% | 79.63% | NA |
| Indica Intermediate | 786 | 55.50% | 1.40% | 3.31% | 39.82% | NA |
| Temperate Japonica | 767 | 71.60% | 0.00% | 0.39% | 28.03% | NA |
| Tropical Japonica | 504 | 83.30% | 0.00% | 0.60% | 16.07% | NA |
| Japonica Intermediate | 241 | 60.60% | 0.00% | 1.24% | 38.17% | NA |
| VI/Aromatic | 96 | 10.40% | 0.00% | 2.08% | 87.50% | NA |
| Intermediate | 90 | 72.20% | 0.00% | 1.11% | 26.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0100790779 | G -> A | LOC_Os01g02430.1 | upstream_gene_variant ; 2160.0bp to feature; MODIFIER | silent_mutation | Average:28.972; most accessible tissue: Callus, score: 77.386 | N | N | N | N |
| vg0100790779 | G -> A | LOC_Os01g02460.1 | upstream_gene_variant ; 3720.0bp to feature; MODIFIER | silent_mutation | Average:28.972; most accessible tissue: Callus, score: 77.386 | N | N | N | N |
| vg0100790779 | G -> A | LOC_Os01g02450.1 | downstream_gene_variant ; 2309.0bp to feature; MODIFIER | silent_mutation | Average:28.972; most accessible tissue: Callus, score: 77.386 | N | N | N | N |
| vg0100790779 | G -> A | LOC_Os01g02440.1 | intron_variant ; MODIFIER | silent_mutation | Average:28.972; most accessible tissue: Callus, score: 77.386 | N | N | N | N |
| vg0100790779 | G -> DEL | N | N | silent_mutation | Average:28.972; most accessible tissue: Callus, score: 77.386 | N | N | N | N |