| Variant ID: vg1007739863 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7739863 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TGGAGGTGATGGTGAACGCTGCCATCTCCTCCAAGCAGCTCTCAAGAAACACACGAACCTCCATATCGGTCCACCGGCTACGGCCATCGCCCATCTACTC[C/T]
GTGCAAGTCAAATAAAATTGAATCGGAAATGAACAAATTAATACAAACAAATACCTTAGATGACTCTTCCTCGCGGACGACGTCCCAATCAATCGAACGG
CCGTTCGATTGATTGGGACGTCGTCCGCGAGGAAGAGTCATCTAAGGTATTTGTTTGTATTAATTTGTTCATTTCCGATTCAATTTTATTTGACTTGCAC[G/A]
GAGTAGATGGGCGATGGCCGTAGCCGGTGGACCGATATGGAGGTTCGTGTGTTTCTTGAGAGCTGCTTGGAGGAGATGGCAGCGTTCACCATCACCTCCA
| 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 | 93.70% | 0.00% | 0.23% | 6.07% | NA |
| All Indica | 2759 | 99.30% | 0.00% | 0.18% | 0.54% | NA |
| All Japonica | 1512 | 81.90% | 0.00% | 0.33% | 17.72% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.30% | 0.00% | 0.65% | 1.08% | NA |
| Indica III | 913 | 99.50% | 0.00% | 0.00% | 0.55% | NA |
| Indica Intermediate | 786 | 99.10% | 0.00% | 0.25% | 0.64% | NA |
| Temperate Japonica | 767 | 82.30% | 0.00% | 0.52% | 17.21% | NA |
| Tropical Japonica | 504 | 84.50% | 0.00% | 0.20% | 15.28% | NA |
| Japonica Intermediate | 241 | 75.50% | 0.00% | 0.00% | 24.48% | NA |
| VI/Aromatic | 96 | 96.90% | 2.10% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 0.00% | 0.00% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1007739863 | C -> T | LOC_Os10g14290.1 | splice_region_variant&intron_variant ; LOW | silent_mutation | Average:5.203; most accessible tissue: Callus, score: 12.562 | N | N | N | N |
| vg1007739863 | C -> T | LOC_Os10g14280.1 | upstream_gene_variant ; 1850.0bp to feature; MODIFIER | silent_mutation | Average:5.203; most accessible tissue: Callus, score: 12.562 | N | N | N | N |
| vg1007739863 | C -> T | LOC_Os10g14270.1 | downstream_gene_variant ; 3806.0bp to feature; MODIFIER | silent_mutation | Average:5.203; most accessible tissue: Callus, score: 12.562 | N | N | N | N |
| vg1007739863 | C -> T | LOC_Os10g14295.1 | downstream_gene_variant ; 1467.0bp to feature; MODIFIER | silent_mutation | Average:5.203; most accessible tissue: Callus, score: 12.562 | N | N | N | N |
| vg1007739863 | C -> DEL | N | N | silent_mutation | Average:5.203; most accessible tissue: Callus, score: 12.562 | N | N | N | N |