| Variant ID: vg0302880531 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr03 | Position: 2880531 |
| Reference Allele: ACT | Alternative Allele: ACTCT,A |
| Primary Allele: ACTCT | Secondary Allele: ACT |
Inferred Ancestral Allele: Not determined.
GAAGAAGAAGAAGAAGAAGAAGATGCCGCGCTGCTAGCTGAGCCGTTCGCACGGCGGCCTGATCGAGCGCGCATTGCCATTTATCGTTTTTGATTTTCTC[ACT/ACTCT,A]
CTCTCTCTCGCCTGTTTGTAGAAGGGACGAGCATACTACTACCGCTAATTACTAGGCTTAATTTTGCAAGTAATGTCGTGTCGAGTTTTTTTTAACAGCG
CGCTGTTAAAAAAAACTCGACACGACATTACTTGCAAAATTAAGCCTAGTAATTAGCGGTAGTAGTATGCTCGTCCCTTCTACAAACAGGCGAGAGAGAG[AGT/AGAGT,T]
GAGAAAATCAAAAACGATAAATGGCAATGCGCGCTCGATCAGGCCGCCGTGCGAACGGCTCAGCTAGCAGCGCGGCATCTTCTTCTTCTTCTTCTTCTTC
| Populations | Population Size | Frequency of ACTCT(primary allele) | Frequency of ACT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 56.20% | 39.90% | 2.39% | 1.48% | A: 0.06% |
| All Indica | 2759 | 89.00% | 4.80% | 3.95% | 2.28% | NA |
| All Japonica | 1512 | 0.30% | 99.50% | 0.07% | 0.00% | A: 0.07% |
| Aus | 269 | 48.00% | 51.30% | 0.00% | 0.74% | NA |
| Indica I | 595 | 87.10% | 3.00% | 8.40% | 1.51% | NA |
| Indica II | 465 | 86.70% | 6.70% | 4.09% | 2.58% | NA |
| Indica III | 913 | 94.30% | 1.20% | 0.99% | 3.50% | NA |
| Indica Intermediate | 786 | 85.60% | 9.20% | 3.94% | 1.27% | NA |
| Temperate Japonica | 767 | 0.30% | 99.70% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 0.20% | 99.40% | 0.20% | 0.00% | A: 0.20% |
| Japonica Intermediate | 241 | 0.80% | 99.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 34.40% | 64.60% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 36.70% | 53.30% | 3.33% | 4.44% | A: 2.22% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0302880531 | ACT -> A | LOC_Os03g05770.1 | 3_prime_UTR_variant ; 125.0bp to feature; MODIFIER | silent_mutation | Average:57.763; most accessible tissue: Callus, score: 83.477 | N | N | N | N |
| vg0302880531 | ACT -> A | LOC_Os03g05780.1 | downstream_gene_variant ; 2473.0bp to feature; MODIFIER | silent_mutation | Average:57.763; most accessible tissue: Callus, score: 83.477 | N | N | N | N |
| vg0302880531 | ACT -> DEL | N | N | silent_mutation | Average:57.763; most accessible tissue: Callus, score: 83.477 | N | N | N | N |
| vg0302880531 | ACT -> ACTCT | LOC_Os03g05770.1 | 3_prime_UTR_variant ; 127.0bp to feature; MODIFIER | silent_mutation | Average:57.763; most accessible tissue: Callus, score: 83.477 | N | N | N | N |
| vg0302880531 | ACT -> ACTCT | LOC_Os03g05780.1 | downstream_gene_variant ; 2471.0bp to feature; MODIFIER | silent_mutation | Average:57.763; most accessible tissue: Callus, score: 83.477 | N | N | N | N |