| Variant ID: vg0137237004 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 37237004 |
| Reference Allele: G | Alternative Allele: A,T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AGTGTGTGACTGTGCTGCGACGTATTTATAATACTTCCTCCGTTCCATAATGTACATTATGTTATTCTAGCATTTTCTATATCCATATAATATAGATGTG[G/A,T]
AAAATGATAGAATGACTTACATTATGAAACGGATATTTGAGTATATATGTAGCACAGTGATGTGTAGGAGCATGTGTTGATTGCTTTCGGTTACCGGTCA
TGACCGGTAACCGAAAGCAATCAACACATGCTCCTACACATCACTGTGCTACATATATACTCAAATATCCGTTTCATAATGTAAGTCATTCTATCATTTT[C/T,A]
CACATCTATATTATATGGATATAGAAAATGCTAGAATAACATAATGTACATTATGGAACGGAGGAAGTATTATAAATACGTCGCAGCACAGTCACACACT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.80% | 0.10% | 0.06% | 0.00% | A: 0.06% |
| All Indica | 2759 | 99.70% | 0.20% | 0.07% | 0.00% | A: 0.07% |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 99.30% | 0.00% | 0.37% | 0.00% | A: 0.37% |
| Indica I | 595 | 98.80% | 0.80% | 0.34% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.00% | 0.00% | 0.00% | A: 0.11% |
| Indica Intermediate | 786 | 99.90% | 0.00% | 0.00% | 0.00% | A: 0.13% |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 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 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0137237004 | G -> T | LOC_Os01g64100.1 | 3_prime_UTR_variant ; 179.0bp to feature; MODIFIER | N | Average:77.274; most accessible tissue: Callus, score: 91.532 | N | N | N | N |
| vg0137237004 | G -> T | LOC_Os01g64110.1 | upstream_gene_variant ; 1897.0bp to feature; MODIFIER | N | Average:77.274; most accessible tissue: Callus, score: 91.532 | N | N | N | N |
| vg0137237004 | G -> T | LOC_Os01g64120.1 | upstream_gene_variant ; 4151.0bp to feature; MODIFIER | N | Average:77.274; most accessible tissue: Callus, score: 91.532 | N | N | N | N |
| vg0137237004 | G -> T | LOC_Os01g64090.1 | downstream_gene_variant ; 2629.0bp to feature; MODIFIER | N | Average:77.274; most accessible tissue: Callus, score: 91.532 | N | N | N | N |
| vg0137237004 | G -> A | LOC_Os01g64100.1 | 3_prime_UTR_variant ; 179.0bp to feature; MODIFIER | N | Average:77.274; most accessible tissue: Callus, score: 91.532 | N | N | N | N |
| vg0137237004 | G -> A | LOC_Os01g64110.1 | upstream_gene_variant ; 1897.0bp to feature; MODIFIER | N | Average:77.274; most accessible tissue: Callus, score: 91.532 | N | N | N | N |
| vg0137237004 | G -> A | LOC_Os01g64120.1 | upstream_gene_variant ; 4151.0bp to feature; MODIFIER | N | Average:77.274; most accessible tissue: Callus, score: 91.532 | N | N | N | N |
| vg0137237004 | G -> A | LOC_Os01g64090.1 | downstream_gene_variant ; 2629.0bp to feature; MODIFIER | N | Average:77.274; most accessible tissue: Callus, score: 91.532 | N | N | N | N |