| Variant ID: vg0137499526 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 37499526 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GGACTTGGAATGGCGGGAGGGACGCGACGGGATCTCGCTGAAACAAAAGAAAAAACCAGAAGACGAACAAGATGGGTGAGTGAAAACTCGCGTTGAGAGA[T/A]
TGAATACAGCCACGACGGGTGAGAGACGAACCTGCGAGGGGGTCGGTTAAACGACCACTTTGGAGGGGAAATAAGGTTTCCCCGAGATGGTTCTGTCTCC
GGAGACAGAACCATCTCGGGGAAACCTTATTTCCCCTCCAAAGTGGTCGTTTAACCGACCCCCTCGCAGGTTCGTCTCTCACCCGTCGTGGCTGTATTCA[A/T]
TCTCTCAACGCGAGTTTTCACTCACCCATCTTGTTCGTCTTCTGGTTTTTTCTTTTGTTTCAGCGAGATCCCGTCGCGTCCCTCCCGCCATTCCAAGTCC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 7.40% | 3.20% | 6.37% | 83.01% | NA |
| All Indica | 2759 | 0.10% | 0.30% | 0.98% | 98.55% | NA |
| All Japonica | 1512 | 22.10% | 8.70% | 14.15% | 55.09% | NA |
| Aus | 269 | 0.00% | 0.00% | 0.37% | 99.63% | NA |
| Indica I | 595 | 0.00% | 0.00% | 0.34% | 99.66% | NA |
| Indica II | 465 | 0.20% | 0.40% | 0.22% | 99.14% | NA |
| Indica III | 913 | 0.00% | 0.20% | 0.33% | 99.45% | NA |
| Indica Intermediate | 786 | 0.40% | 0.60% | 2.67% | 96.31% | NA |
| Temperate Japonica | 767 | 39.90% | 0.80% | 11.86% | 47.46% | NA |
| Tropical Japonica | 504 | 0.80% | 24.20% | 16.47% | 58.53% | NA |
| Japonica Intermediate | 241 | 10.00% | 1.20% | 16.60% | 72.20% | NA |
| VI/Aromatic | 96 | 0.00% | 4.20% | 44.79% | 51.04% | NA |
| Intermediate | 90 | 14.40% | 7.80% | 17.78% | 60.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0137499526 | T -> A | LOC_Os01g64600.1 | downstream_gene_variant ; 2641.0bp to feature; MODIFIER | silent_mutation | Average:6.502; most accessible tissue: Callus, score: 16.181 | N | N | N | N |
| vg0137499526 | T -> A | LOC_Os01g64610.1 | intron_variant ; MODIFIER | silent_mutation | Average:6.502; most accessible tissue: Callus, score: 16.181 | N | N | N | N |
| vg0137499526 | T -> DEL | N | N | silent_mutation | Average:6.502; most accessible tissue: Callus, score: 16.181 | N | N | N | N |