| Variant ID: vg0722037042 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 22037042 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.00, others allele: 0.00, population size: 313. )
TGCAGTCAGGCCTCCTCATAGGTTAAACATAAAAATTCTAATACATGGTGGATGGCTCAATGTGTTAGTTCGTGATAGCTCAATTATGTGCTATTAATAT[A/G]
CAGAAGGCATGGAACTACAGAACTACAGAAAAGCATAGCATATGTACAACATGAGTCACTCATATTACTCTCAAATACGTAAATGTCTTTCCCTAATCAA
TTGATTAGGGAAAGACATTTACGTATTTGAGAGTAATATGAGTGACTCATGTTGTACATATGCTATGCTTTTCTGTAGTTCTGTAGTTCCATGCCTTCTG[T/C]
ATATTAATAGCACATAATTGAGCTATCACGAACTAACACATTGAGCCATCCACCATGTATTAGAATTTTTATGTTTAACCTATGAGGAGGCCTGACTGCA
| 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 | 97.60% | 2.40% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 63.90% | 36.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.60% | 1.40% | 0.00% | 0.00% | NA |
| 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 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0722037042 | A -> G | LOC_Os07g36780.1 | 3_prime_UTR_variant ; 118.0bp to feature; MODIFIER | silent_mutation | Average:53.694; most accessible tissue: Callus, score: 83.434 | N | N | N | N |
| vg0722037042 | A -> G | LOC_Os07g36770.1 | upstream_gene_variant ; 2182.0bp to feature; MODIFIER | silent_mutation | Average:53.694; most accessible tissue: Callus, score: 83.434 | N | N | N | N |