| Variant ID: vg0137237014 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 37237014 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TGTGCTGCGACGTATTTATAATACTTCCTCCGTTCCATAATGTACATTATGTTATTCTAGCATTTTCTATATCCATATAATATAGATGTGGAAAATGATA[G/A]
AATGACTTACATTATGAAACGGATATTTGAGTATATATGTAGCACAGTGATGTGTAGGAGCATGTGTTGATTGCTTTCGGTTACCGGTCAGACGTTTAGA
TCTAAACGTCTGACCGGTAACCGAAAGCAATCAACACATGCTCCTACACATCACTGTGCTACATATATACTCAAATATCCGTTTCATAATGTAAGTCATT[C/T]
TATCATTTTCCACATCTATATTATATGGATATAGAAAATGCTAGAATAACATAATGTACATTATGGAACGGAGGAAGTATTATAAATACGTCGCAGCACA
| 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 | 64.40% | 35.30% | 0.06% | 0.23% | NA |
| All Indica | 2759 | 98.20% | 1.50% | 0.07% | 0.25% | NA |
| All Japonica | 1512 | 2.10% | 97.80% | 0.00% | 0.13% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.50% | 0.00% | 0.17% | 0.34% | NA |
| Indica II | 465 | 98.70% | 0.90% | 0.00% | 0.43% | NA |
| Indica III | 913 | 99.10% | 0.70% | 0.11% | 0.11% | NA |
| Indica Intermediate | 786 | 95.70% | 4.10% | 0.00% | 0.25% | NA |
| Temperate Japonica | 767 | 1.40% | 98.40% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 3.00% | 96.80% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 2.10% | 97.90% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 2.10% | 96.90% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 38.90% | 58.90% | 0.00% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0137237014 | G -> A | LOC_Os01g64100.1 | 3_prime_UTR_variant ; 189.0bp to feature; MODIFIER | silent_mutation | Average:75.799; most accessible tissue: Callus, score: 91.532 | N | N | N | N |
| vg0137237014 | G -> A | LOC_Os01g64110.1 | upstream_gene_variant ; 1887.0bp to feature; MODIFIER | silent_mutation | Average:75.799; most accessible tissue: Callus, score: 91.532 | N | N | N | N |
| vg0137237014 | G -> A | LOC_Os01g64120.1 | upstream_gene_variant ; 4141.0bp to feature; MODIFIER | silent_mutation | Average:75.799; most accessible tissue: Callus, score: 91.532 | N | N | N | N |
| vg0137237014 | G -> A | LOC_Os01g64090.1 | downstream_gene_variant ; 2639.0bp to feature; MODIFIER | silent_mutation | Average:75.799; most accessible tissue: Callus, score: 91.532 | N | N | N | N |
| vg0137237014 | G -> DEL | N | N | silent_mutation | Average:75.799; most accessible tissue: Callus, score: 91.532 | N | N | N | N |