| Variant ID: vg0234179855 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 34179855 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 318. )
TTCCTTCAAACACGTAATGGCCCAAAAAACAGTGACGGCCAGCCAATACTGACTGATCATACCTGGCACATTGTTGAAAGGTTCAATCAATTTCTTGAAA[C/T]
GTTTCATGACTGTACTCTTCTGTTATCTCAAGTATATTATCCAACAGCTAATTTAATTTTGCATAATATTCTTGAAATTGCCACTTTGTTGAAAGAGTAT
ATACTCTTTCAACAAAGTGGCAATTTCAAGAATATTATGCAAAATTAAATTAGCTGTTGGATAATATACTTGAGATAACAGAAGAGTACAGTCATGAAAC[G/A]
TTTCAAGAAATTGATTGAACCTTTCAACAATGTGCCAGGTATGATCAGTCAGTATTGGCTGGCCGTCACTGTTTTTTGGGCCATTACGTGTTTGAAGGAA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 54.20% | 0.10% | 6.67% | 39.04% | NA |
| All Indica | 2759 | 31.80% | 0.10% | 8.26% | 59.84% | NA |
| All Japonica | 1512 | 97.60% | 0.00% | 0.26% | 2.12% | NA |
| Aus | 269 | 44.20% | 0.00% | 23.05% | 32.71% | NA |
| Indica I | 595 | 23.70% | 0.00% | 3.70% | 72.61% | NA |
| Indica II | 465 | 24.90% | 0.00% | 4.73% | 70.32% | NA |
| Indica III | 913 | 38.70% | 0.20% | 15.01% | 46.11% | NA |
| Indica Intermediate | 786 | 34.10% | 0.00% | 5.98% | 59.92% | NA |
| Temperate Japonica | 767 | 97.50% | 0.00% | 0.26% | 2.22% | NA |
| Tropical Japonica | 504 | 99.40% | 0.00% | 0.00% | 0.60% | NA |
| Japonica Intermediate | 241 | 94.20% | 0.00% | 0.83% | 4.98% | NA |
| VI/Aromatic | 96 | 30.20% | 3.10% | 16.67% | 50.00% | NA |
| Intermediate | 90 | 65.60% | 0.00% | 5.56% | 28.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0234179855 | C -> T | LOC_Os02g55840.1 | upstream_gene_variant ; 2230.0bp to feature; MODIFIER | silent_mutation | Average:4.505; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0234179855 | C -> T | LOC_Os02g55840.2 | upstream_gene_variant ; 2230.0bp to feature; MODIFIER | silent_mutation | Average:4.505; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0234179855 | C -> T | LOC_Os02g55840.5 | upstream_gene_variant ; 2230.0bp to feature; MODIFIER | silent_mutation | Average:4.505; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0234179855 | C -> T | LOC_Os02g55840.4 | upstream_gene_variant ; 2230.0bp to feature; MODIFIER | silent_mutation | Average:4.505; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0234179855 | C -> T | LOC_Os02g55840.3 | upstream_gene_variant ; 2230.0bp to feature; MODIFIER | silent_mutation | Average:4.505; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0234179855 | C -> T | LOC_Os02g55840.6 | upstream_gene_variant ; 2232.0bp to feature; MODIFIER | silent_mutation | Average:4.505; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0234179855 | C -> T | LOC_Os02g55830.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.505; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0234179855 | C -> DEL | N | N | silent_mutation | Average:4.505; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |