| Variant ID: vg0108457621 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 8457621 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 259. )
CTTGAAGGATAGGCATGGCTATTCCCCTACGGTGTCTCCGGATACCGTCAGGAGATACGAAAGCGCTATCTCTGATCTCGCCGGGCACAGATTCGAGGAG[G/T]
AAGACTACCCTGTTGTCGACTACGAGTCAGACCTTCAGACCGACATGTCCACAACAGTTAGATAGGCTACCCACATATTGTACTGGTGTGATTATGGTGA
TCACCATAATCACACCAGTACAATATGTGGGTAGCCTATCTAACTGTTGTGGACATGTCGGTCTGAAGGTCTGACTCGTAGTCGACAACAGGGTAGTCTT[C/A]
CTCCTCGAATCTGTGCCCGGCGAGATCAGAGATAGCGCTTTCGTATCTCCTGACGGTATCCGGAGACACCGTAGGGGAATAGCCATGCCTATCCTTCAAG
| 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% | 0.20% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0108457621 | G -> T | LOC_Os01g15070.1 | stop_gained ; p.Glu66*; HIGH | N | Average:51.322; most accessible tissue: Zhenshan97 panicle, score: 68.538 | N | N | N | N |
| vg0108457621 | G -> T | LOC_Os01g15080.1 | upstream_gene_variant ; 338.0bp to feature; MODIFIER | N | Average:51.322; most accessible tissue: Zhenshan97 panicle, score: 68.538 | N | N | N | N |
| vg0108457621 | G -> T | LOC_Os01g15090.1 | upstream_gene_variant ; 3451.0bp to feature; MODIFIER | N | Average:51.322; most accessible tissue: Zhenshan97 panicle, score: 68.538 | N | N | N | N |
| vg0108457621 | G -> T | LOC_Os01g15060.1 | downstream_gene_variant ; 1599.0bp to feature; MODIFIER | N | Average:51.322; most accessible tissue: Zhenshan97 panicle, score: 68.538 | N | N | N | N |