| Variant ID: vg0234310872 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 34310872 |
| Reference Allele: TA | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: TA |
Inferred Ancestral Allele: Not determined.
ACGACAAGTACATTTACATGTACCTATGAAGATAATATACCTATACCTATGGAATTCCTCTACTTATTCTACTGTAGTTGGTAATTTTCTTCATTTTTTT[TA/T]
AGATAATGAAATAACATTCCGGCTTTTGCTCAACGAGATACAACCAATTATTACAAAGTCCACACACGAACAAACTCAGCACACACTGACATAATGTAAA
TTTACATTATGTCAGTGTGTGCTGAGTTTGTTCGTGTGTGGACTTTGTAATAATTGGTTGTATCTCGTTGAGCAAAAGCCGGAATGTTATTTCATTATCT[TA/A]
AAAAAAATGAAGAAAATTACCAACTACAGTAGAATAAGTAGAGGAATTCCATAGGTATAGGTATATTATCTTCATAGGTACATGTAAATGTACTTGTCGT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of TA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 68.00% | 32.00% | 0.04% | 0.00% | NA |
| All Indica | 2759 | 98.70% | 1.30% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 6.40% | 93.60% | 0.00% | 0.00% | NA |
| Aus | 269 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.10% | 1.70% | 0.22% | 0.00% | NA |
| Indica III | 913 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.20% | 1.80% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 3.00% | 97.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 11.30% | 88.70% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 7.10% | 92.90% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 79.20% | 20.80% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 56.70% | 42.20% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0234310872 | TA -> T | LOC_Os02g56040.1 | upstream_gene_variant ; 3144.0bp to feature; MODIFIER | silent_mutation | Average:37.761; most accessible tissue: Callus, score: 59.39 | N | N | N | N |
| vg0234310872 | TA -> T | LOC_Os02g56060.1 | upstream_gene_variant ; 1833.0bp to feature; MODIFIER | silent_mutation | Average:37.761; most accessible tissue: Callus, score: 59.39 | N | N | N | N |
| vg0234310872 | TA -> T | LOC_Os02g56050.1 | intron_variant ; MODIFIER | silent_mutation | Average:37.761; most accessible tissue: Callus, score: 59.39 | N | N | N | N |