| Variant ID: vg0137237010 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 37237010 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TGACTGTGCTGCGACGTATTTATAATACTTCCTCCGTTCCATAATGTACATTATGTTATTCTAGCATTTTCTATATCCATATAATATAGATGTGGAAAAT[G/A]
ATAGAATGACTTACATTATGAAACGGATATTTGAGTATATATGTAGCACAGTGATGTGTAGGAGCATGTGTTGATTGCTTTCGGTTACCGGTCAGACGTT
AACGTCTGACCGGTAACCGAAAGCAATCAACACATGCTCCTACACATCACTGTGCTACATATATACTCAAATATCCGTTTCATAATGTAAGTCATTCTAT[C/T]
ATTTTCCACATCTATATTATATGGATATAGAAAATGCTAGAATAACATAATGTACATTATGGAACGGAGGAAGTATTATAAATACGTCGCAGCACAGTCA
| 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 | 80.50% | 19.50% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 74.20% | 25.70% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 25.70% | 74.30% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.00% | 2.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 85.40% | 14.40% | 0.22% | 0.00% | NA |
| Indica III | 913 | 57.10% | 42.90% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 69.60% | 30.40% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 90.00% | 10.00% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0137237010 | G -> A | LOC_Os01g64100.1 | 3_prime_UTR_variant ; 185.0bp to feature; MODIFIER | silent_mutation | Average:76.455; most accessible tissue: Callus, score: 91.532 | N | N | N | N |
| vg0137237010 | G -> A | LOC_Os01g64110.1 | upstream_gene_variant ; 1891.0bp to feature; MODIFIER | silent_mutation | Average:76.455; most accessible tissue: Callus, score: 91.532 | N | N | N | N |
| vg0137237010 | G -> A | LOC_Os01g64120.1 | upstream_gene_variant ; 4145.0bp to feature; MODIFIER | silent_mutation | Average:76.455; most accessible tissue: Callus, score: 91.532 | N | N | N | N |
| vg0137237010 | G -> A | LOC_Os01g64090.1 | downstream_gene_variant ; 2635.0bp to feature; MODIFIER | silent_mutation | Average:76.455; most accessible tissue: Callus, score: 91.532 | N | N | N | N |