| Variant ID: vg0114527001 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr01 | Position: 14527001 |
| Reference Allele: TA | Alternative Allele: T |
| Primary Allele: TA | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CGAAAAAGGTTACTATCATGTGCGGATTGCATATTTCCAAGTCTTTGGCTTCATTAATTTTGGCCCTGGTCACAGATGATGATGTTGGAAGACATACGTA[TA/T]
AGTTAATGTACCATGAAAAATATAAATCTATATATAGGCATTACACAAAAAGTATCATAGTATATATCTTGAGTAGGGAACTATTACAAACTAATTTCAT
ATGAAATTAGTTTGTAATAGTTCCCTACTCAAGATATATACTATGATACTTTTTGTGTAATGCCTATATATAGATTTATATTTTTCATGGTACATTAACT[TA/A]
TACGTATGTCTTCCAACATCATCATCTGTGACCAGGGCCAAAATTAATGAAGCCAAAGACTTGGAAATATGCAATCCGCACATGATAGTAACCTTTTTCG
| Populations | Population Size | Frequency of TA(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 95.60% | 0.70% | 0.38% | 3.34% | NA |
| All Indica | 2759 | 92.50% | 1.20% | 0.65% | 5.62% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.00% | 0.07% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.00% | 0.37% | NA |
| Indica I | 595 | 95.50% | 0.00% | 0.34% | 4.20% | NA |
| Indica II | 465 | 97.40% | 0.00% | 0.00% | 2.58% | NA |
| Indica III | 913 | 89.90% | 2.50% | 0.99% | 6.57% | NA |
| Indica Intermediate | 786 | 90.30% | 1.40% | 0.89% | 7.38% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 0.00% | 0.00% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0114527001 | TA -> T | LOC_Os01g25630.1 | intron_variant ; MODIFIER | silent_mutation | Average:48.227; most accessible tissue: Callus, score: 80.0 | N | N | N | N |
| vg0114527001 | TA -> DEL | N | N | silent_mutation | Average:48.227; most accessible tissue: Callus, score: 80.0 | N | N | N | N |