| Variant ID: vg1120444821 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 20444821 |
| Reference Allele: TA | Alternative Allele: T,TAA |
| Primary Allele: TA | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GCCCGGTCCTGTCAATTTAGTGGTCCGGAGCGAAGCTAGAAAGATGGGCCCTTTAATACAACTCTGATAATATAATGATGTTTCTAACAAATGTAATGCA[TA/T,TAA]
AAAAAAACATTCTTAGCAAACAAGTTGTATATCTTCCTCTCCTGTGCTTCCTAAATCTAAGTTCCTATGGCCTATGGGCTCCTATATCCATAGCATACAT
ATGTATGCTATGGATATAGGAGCCCATAGGCCATAGGAACTTAGATTTAGGAAGCACAGGAGAGGAAGATATACAACTTGTTTGCTAAGAATGTTTTTTT[TA/A,TTA]
TGCATTACATTTGTTAGAAACATCATTATATTATCAGAGTTGTATTAAAGGGCCCATCTTTCTAGCTTCGCTCCGGACCACTAAATTGACAGGACCGGGC
| 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 | 70.10% | 4.40% | 1.57% | 20.50% | TAA: 3.47% |
| All Indica | 2759 | 68.00% | 1.60% | 1.30% | 28.56% | TAA: 0.54% |
| All Japonica | 1512 | 83.80% | 1.10% | 1.72% | 3.70% | TAA: 9.66% |
| Aus | 269 | 7.10% | 52.40% | 4.09% | 36.43% | NA |
| Indica I | 595 | 52.10% | 0.00% | 1.18% | 46.55% | TAA: 0.17% |
| Indica II | 465 | 77.60% | 0.20% | 1.08% | 20.43% | TAA: 0.65% |
| Indica III | 913 | 69.20% | 1.90% | 1.42% | 27.38% | TAA: 0.11% |
| Indica Intermediate | 786 | 72.80% | 3.40% | 1.40% | 21.12% | TAA: 1.27% |
| Temperate Japonica | 767 | 76.40% | 2.20% | 2.87% | 1.04% | TAA: 17.47% |
| Tropical Japonica | 504 | 90.50% | 0.00% | 0.60% | 8.93% | NA |
| Japonica Intermediate | 241 | 93.40% | 0.00% | 0.41% | 1.24% | TAA: 4.98% |
| VI/Aromatic | 96 | 79.20% | 0.00% | 1.04% | 19.79% | NA |
| Intermediate | 90 | 84.40% | 3.30% | 0.00% | 8.89% | TAA: 3.33% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1120444821 | TA -> T | LOC_Os11g34880.1 | 3_prime_UTR_variant ; 302.0bp to feature; MODIFIER | silent_mutation | Average:39.617; most accessible tissue: Callus, score: 69.352 | N | N | N | N |
| vg1120444821 | TA -> TAA | LOC_Os11g34880.1 | 3_prime_UTR_variant ; 301.0bp to feature; MODIFIER | silent_mutation | Average:39.617; most accessible tissue: Callus, score: 69.352 | N | N | N | N |
| vg1120444821 | TA -> DEL | N | N | silent_mutation | Average:39.617; most accessible tissue: Callus, score: 69.352 | N | N | N | N |