| Variant ID: vg0521975499 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 21975499 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TCGAGGATACGCCGCCGCGCGGCGGTGCTGATTTAGGATGGATAAACAAGTGAAGAACCACAGACCTTCTGATGGTACGGATGGATCAAGGTATGTTGTT[C/T]
TGTTTCAGTGATTTATTTCAGTATGTGCCGCTGGTTTTTTTTCTCTGAATTTCGCCGTGTGAACTTGAGCAATTCTAAATCATCAATTCAGGGAAATTCT
AGAATTTCCCTGAATTGATGATTTAGAATTGCTCAAGTTCACACGGCGAAATTCAGAGAAAAAAAACCAGCGGCACATACTGAAATAAATCACTGAAACA[G/A]
AACAACATACCTTGATCCATCCGTACCATCAGAAGGTCTGTGGTTCTTCACTTGTTTATCCATCCTAAATCAGCACCGCCGCGCGGCGGCGTATCCTCGA
| 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 | 37.60% | 0.90% | 8.00% | 53.53% | NA |
| All Indica | 2759 | 3.50% | 0.00% | 10.62% | 85.86% | NA |
| All Japonica | 1512 | 94.20% | 2.80% | 2.12% | 0.86% | NA |
| Aus | 269 | 45.70% | 0.00% | 13.01% | 41.26% | NA |
| Indica I | 595 | 2.50% | 0.00% | 13.61% | 83.87% | NA |
| Indica II | 465 | 5.20% | 0.00% | 5.59% | 89.25% | NA |
| Indica III | 913 | 1.40% | 0.00% | 13.58% | 84.99% | NA |
| Indica Intermediate | 786 | 5.70% | 0.00% | 7.89% | 86.39% | NA |
| Temperate Japonica | 767 | 98.30% | 0.10% | 0.52% | 1.04% | NA |
| Tropical Japonica | 504 | 89.90% | 7.10% | 2.58% | 0.40% | NA |
| Japonica Intermediate | 241 | 90.50% | 2.10% | 6.22% | 1.24% | NA |
| VI/Aromatic | 96 | 84.40% | 0.00% | 13.54% | 2.08% | NA |
| Intermediate | 90 | 54.40% | 1.10% | 5.56% | 38.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0521975499 | C -> T | LOC_Os05g37530.1 | downstream_gene_variant ; 4316.0bp to feature; MODIFIER | silent_mutation | Average:6.787; most accessible tissue: Callus, score: 29.988 | N | N | N | N |
| vg0521975499 | C -> T | LOC_Os05g37550.1 | downstream_gene_variant ; 4588.0bp to feature; MODIFIER | silent_mutation | Average:6.787; most accessible tissue: Callus, score: 29.988 | N | N | N | N |
| vg0521975499 | C -> T | LOC_Os05g37540.1 | intron_variant ; MODIFIER | silent_mutation | Average:6.787; most accessible tissue: Callus, score: 29.988 | N | N | N | N |
| vg0521975499 | C -> DEL | N | N | silent_mutation | Average:6.787; most accessible tissue: Callus, score: 29.988 | N | N | N | N |