| Variant ID: vg0123776149 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 23776149 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GTCCTCGCCAATCTCCAAAGTGTGGCTTCTTCTGACATTGCCTTGGCGCCCTCAGTCCCGCTGCGTTGGCGGTGCTCGAATACTCTCAACCATTCCTTTC[C/T]
TTCCAAATCGACCAAGCCCCGGGAACGATGATGGTATCGAACCCGCACCGTTGCTTTGCCGGTATGGTATGTCGACAATCACACAGCCAGGAGTAGAAGG
CCTTCTACTCCTGGCTGTGTGATTGTCGACATACCATACCGGCAAAGCAACGGTGCGGGTTCGATACCATCATCGTTCCCGGGGCTTGGTCGATTTGGAA[G/A]
GAAAGGAATGGTTGAGAGTATTCGAGCACCGCCAACGCAGCGGGACTGAGGGCGCCAAGGCAATGTCAGAAGAAGCCACACTTTGGAGATTGGCGAGGAC
| 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 | 43.70% | 0.90% | 1.67% | 53.81% | NA |
| All Indica | 2759 | 11.30% | 0.00% | 2.65% | 86.01% | NA |
| All Japonica | 1512 | 92.00% | 0.00% | 0.20% | 7.80% | NA |
| Aus | 269 | 92.20% | 0.00% | 0.00% | 7.81% | NA |
| Indica I | 595 | 4.40% | 0.00% | 2.18% | 93.45% | NA |
| Indica II | 465 | 6.90% | 0.00% | 3.66% | 89.46% | NA |
| Indica III | 913 | 12.50% | 0.00% | 1.86% | 85.65% | NA |
| Indica Intermediate | 786 | 17.90% | 0.00% | 3.31% | 78.75% | NA |
| Temperate Japonica | 767 | 99.50% | 0.00% | 0.00% | 0.52% | NA |
| Tropical Japonica | 504 | 78.80% | 0.00% | 0.60% | 20.63% | NA |
| Japonica Intermediate | 241 | 95.90% | 0.00% | 0.00% | 4.15% | NA |
| VI/Aromatic | 96 | 56.20% | 40.60% | 2.08% | 1.04% | NA |
| Intermediate | 90 | 63.30% | 2.20% | 1.11% | 33.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0123776149 | C -> T | LOC_Os01g41930.1 | 5_prime_UTR_variant ; 353.0bp to feature; MODIFIER | silent_mutation | Average:12.935; most accessible tissue: Callus, score: 73.338 | N | N | N | N |
| vg0123776149 | C -> T | LOC_Os01g41920.1 | upstream_gene_variant ; 3466.0bp to feature; MODIFIER | silent_mutation | Average:12.935; most accessible tissue: Callus, score: 73.338 | N | N | N | N |
| vg0123776149 | C -> T | LOC_Os01g41910.1 | downstream_gene_variant ; 4634.0bp to feature; MODIFIER | silent_mutation | Average:12.935; most accessible tissue: Callus, score: 73.338 | N | N | N | N |
| vg0123776149 | C -> DEL | N | N | silent_mutation | Average:12.935; most accessible tissue: Callus, score: 73.338 | N | N | N | N |