| Variant ID: vg1127724045 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 27724045 |
| Reference Allele: C | Alternative Allele: CCATTTTTT,CCATTTTTTTTGAGAATTAATATTATTTTTATGGAAAA,CCATTTTTTTTGAGAATTAATATTATT,CCATTTTTTTTGAGAA,CCA,CGA |
| Primary Allele: C | Secondary Allele: CCATTTTTTTTGAGAA |
Inferred Ancestral Allele: Not determined.
TGACCAAACGCAGAGGGGAAAATATCGGACTTTGGAAGCTGGAAATGATCCCCAACTCTGACCGCTCGGAGAGCCCGCTCATCCTAACCTGATCTGATGC[C/CCATTTTTT,CCATTTTTTTTGAGAATTAATATTATTTTTATGGAAAA,CCATTTTTTTTGAGAATTAATATTATT,CCATTTTTTTTGAGAA,CCA,CGA]
TTCAGCTTCTAGGTTCAGTAATCCCTCTCTTCTTCGCTTCAGTGATTTATCTAATGCCTTCAACTGCTATTCAGTAATCCCTCTCTAGCTTTGTTTGCTT
AAGCAAACAAAGCTAGAGAGGGATTACTGAATAGCAGTTGAAGGCATTAGATAAATCACTGAAGCGAAGAAGAGAGGGATTACTGAACCTAGAAGCTGAA[G/AAAAAATGG,TTTTCCATAAAAATAATATTAATTCTCAAAAAAAATGG,AATAATATTAATTCTCAAAAAAAATGG,TTCTCAAAAAAAATGG,TGG,TCG]
GCATCAGATCAGGTTAGGATGAGCGGGCTCTCCGAGCGGTCAGAGTTGGGGATCATTTCCAGCTTCCAAAGTCCGATATTTTCCCCTCTGCGTTTGGTCA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of CCATTTTTTTTGAGAA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 72.40% | 0.10% | 1.69% | 25.77% | CCATTTTTT: 0.04%; CCATTTTTTTTGAGAATTAATATTATT: 0.04%; CCA: 0.02% |
| All Indica | 2759 | 73.40% | 0.10% | 1.20% | 25.15% | CCATTTTTT: 0.07%; CCATTTTTTTTGAGAATTAATATTATT: 0.07%; CCA: 0.04% |
| All Japonica | 1512 | 79.60% | 0.00% | 2.78% | 17.59% | NA |
| Aus | 269 | 32.30% | 0.00% | 0.74% | 66.91% | NA |
| Indica I | 595 | 64.20% | 0.20% | 3.53% | 32.10% | NA |
| Indica II | 465 | 68.20% | 0.00% | 0.43% | 31.18% | CCATTTTTT: 0.22% |
| Indica III | 913 | 86.20% | 0.00% | 0.44% | 13.25% | CCATTTTTTTTGAGAATTAATATTATT: 0.11% |
| Indica Intermediate | 786 | 68.40% | 0.30% | 0.76% | 30.15% | CCATTTTTTTTGAGAATTAATATTATT: 0.13%; CCATTTTTT: 0.13%; CCA: 0.13% |
| Temperate Japonica | 767 | 82.90% | 0.00% | 3.52% | 13.56% | NA |
| Tropical Japonica | 504 | 71.60% | 0.00% | 0.60% | 27.78% | NA |
| Japonica Intermediate | 241 | 85.90% | 0.00% | 4.98% | 9.13% | NA |
| VI/Aromatic | 96 | 35.40% | 0.00% | 1.04% | 63.54% | NA |
| Intermediate | 90 | 78.90% | 0.00% | 2.22% | 18.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1127724045 | C -> CCATTTTTT | LOC_Os11g45820.1 | 5_prime_UTR_variant ; 198.0bp to feature; MODIFIER | silent_mutation | Average:50.905; most accessible tissue: Callus, score: 95.085 | N | N | N | N |
| vg1127724045 | C -> CCATTTTTT | LOC_Os11g45809.1 | downstream_gene_variant ; 2946.0bp to feature; MODIFIER | silent_mutation | Average:50.905; most accessible tissue: Callus, score: 95.085 | N | N | N | N |
| vg1127724045 | C -> CCATTTTTTTTGAGAA | LOC_Os11g45820.1 | 5_prime_UTR_variant ; 198.0bp to feature; MODIFIER | silent_mutation | Average:50.905; most accessible tissue: Callus, score: 95.085 | N | N | N | N |
| vg1127724045 | C -> CCATTTTTTTTGAGAA | LOC_Os11g45809.1 | downstream_gene_variant ; 2946.0bp to feature; MODIFIER | silent_mutation | Average:50.905; most accessible tissue: Callus, score: 95.085 | N | N | N | N |
| vg1127724045 | C -> DEL | N | N | silent_mutation | Average:50.905; most accessible tissue: Callus, score: 95.085 | N | N | N | N |
| vg1127724045 | C -> CCA | LOC_Os11g45820.1 | 5_prime_UTR_variant ; 198.0bp to feature; MODIFIER | silent_mutation | Average:50.905; most accessible tissue: Callus, score: 95.085 | N | N | N | N |
| vg1127724045 | C -> CCA | LOC_Os11g45809.1 | downstream_gene_variant ; 2946.0bp to feature; MODIFIER | silent_mutation | Average:50.905; most accessible tissue: Callus, score: 95.085 | N | N | N | N |
| vg1127724045 | C -> CGA | LOC_Os11g45820.1 | 5_prime_UTR_variant ; 198.0bp to feature; MODIFIER | N | Average:50.905; most accessible tissue: Callus, score: 95.085 | N | N | N | N |
| vg1127724045 | C -> CGA | LOC_Os11g45809.1 | downstream_gene_variant ; 2946.0bp to feature; MODIFIER | N | Average:50.905; most accessible tissue: Callus, score: 95.085 | N | N | N | N |
| vg1127724045 | C -> CCATTTTTTTTGAGAATTAATATTATT | LOC_Os11g45820.1 | 5_prime_UTR_variant ; 198.0bp to feature; MODIFIER | silent_mutation | Average:50.905; most accessible tissue: Callus, score: 95.085 | N | N | N | N |
| vg1127724045 | C -> CCATTTTTTTTGAGAATTAATATTATT | LOC_Os11g45809.1 | downstream_gene_variant ; 2946.0bp to feature; MODIFIER | silent_mutation | Average:50.905; most accessible tissue: Callus, score: 95.085 | N | N | N | N |
| vg1127724045 | C -> CCATTTTTTTTGAGAATTAATATTATTTTT ATGGAAAA | LOC_Os11g45820.1 | 5_prime_UTR_variant ; 198.0bp to feature; MODIFIER | N | Average:50.905; most accessible tissue: Callus, score: 95.085 | N | N | N | N |
| vg1127724045 | C -> CCATTTTTTTTGAGAATTAATATTATTTTT ATGGAAAA | LOC_Os11g45809.1 | downstream_gene_variant ; 2946.0bp to feature; MODIFIER | N | Average:50.905; most accessible tissue: Callus, score: 95.085 | N | N | N | N |
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