| Variant ID: vg0426093767 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 26093767 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GAAATCAATAGCTAATGTTTCTATTCATGACGTGTCTACCAGGGAGGATTTACATAATTAGAGTCGGGGACTTTTTTGGGGCCTTTTGTGGGTTGACTCC[A/C]
AAAAAAAAAAAAAAATCCCAATGAGAACCTTTAAAAAAAACAGAATGATCTATTTTGGTTTACTTAATGATCAATGCGCCTATGATTGCATGCATCTGTT
AACAGATGCATGCAATCATAGGCGCATTGATCATTAAGTAAACCAAAATAGATCATTCTGTTTTTTTTAAAGGTTCTCATTGGGATTTTTTTTTTTTTTT[T/G]
GGAGTCAACCCACAAAAGGCCCCAAAAAAGTCCCCGACTCTAATTATGTAAATCCTCCCTGGTAGACACGTCATGAATAGAAACATTAGCTATTGATTTC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 93.70% | 2.10% | 4.21% | 0.00% | NA |
| All Indica | 2759 | 93.70% | 1.80% | 4.46% | 0.00% | NA |
| All Japonica | 1512 | 93.10% | 2.80% | 4.17% | 0.00% | NA |
| Aus | 269 | 95.20% | 1.50% | 3.35% | 0.00% | NA |
| Indica I | 595 | 93.60% | 0.80% | 5.55% | 0.00% | NA |
| Indica II | 465 | 92.50% | 1.90% | 5.59% | 0.00% | NA |
| Indica III | 913 | 95.20% | 2.20% | 2.63% | 0.00% | NA |
| Indica Intermediate | 786 | 92.70% | 2.20% | 5.09% | 0.00% | NA |
| Temperate Japonica | 767 | 93.40% | 1.60% | 5.08% | 0.00% | NA |
| Tropical Japonica | 504 | 92.10% | 4.80% | 3.17% | 0.00% | NA |
| Japonica Intermediate | 241 | 94.20% | 2.50% | 3.32% | 0.00% | NA |
| VI/Aromatic | 96 | 94.80% | 1.00% | 4.17% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0426093767 | A -> C | LOC_Os04g44030.1 | 3_prime_UTR_variant ; 1630.0bp to feature; MODIFIER | silent_mutation | Average:48.113; most accessible tissue: Callus, score: 84.682 | N | N | N | N |
| vg0426093767 | A -> C | LOC_Os04g44050.1 | upstream_gene_variant ; 3942.0bp to feature; MODIFIER | silent_mutation | Average:48.113; most accessible tissue: Callus, score: 84.682 | N | N | N | N |