| Variant ID: vg0607893786 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr06 | Position: 7893786 |
| Reference Allele: T | Alternative Allele: C,TC |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CGACCCCCTCGCAGGTTCGTCTCTCACCCATCGTGGCTGTATTCATTCTCTCAACGCGAGTTTTCACTCACCCATCTTGTTCGTCTTCTGGTCTTTTCTT[T/C,TC]
TGTTTCAGCGAGATCCCGTCGCGTCCCTCCCGCCATTCCAAGTCCGGCCAGTCTGAGGCCGAGGATCCGGCGACCGCAGAGGCCCGCAGGCGGCAAGCTG
CAGCTTGCCGCCTGCGGGCCTCTGCGGTCGCCGGATCCTCGGCCTCAGACTGGCCGGACTTGGAATGGCGGGAGGGACGCGACGGGATCTCGCTGAAACA[A/G,GA]
AAGAAAAGACCAGAAGACGAACAAGATGGGTGAGTGAAAACTCGCGTTGAGAGAATGAATACAGCCACGATGGGTGAGAGACGAACCTGCGAGGGGGTCG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 6.90% | 0.20% | 1.86% | 90.99% | NA |
| All Indica | 2759 | 0.40% | 0.40% | 2.32% | 96.88% | NA |
| All Japonica | 1512 | 20.20% | 0.00% | 0.53% | 79.30% | NA |
| Aus | 269 | 0.00% | 0.00% | 5.58% | 94.42% | NA |
| Indica I | 595 | 0.30% | 0.00% | 1.18% | 98.49% | NA |
| Indica II | 465 | 0.20% | 0.00% | 0.65% | 99.14% | NA |
| Indica III | 913 | 0.90% | 1.00% | 4.71% | 93.43% | NA |
| Indica Intermediate | 786 | 0.00% | 0.30% | 1.40% | 98.35% | NA |
| Temperate Japonica | 767 | 34.40% | 0.00% | 0.00% | 65.58% | NA |
| Tropical Japonica | 504 | 3.40% | 0.00% | 1.39% | 95.24% | NA |
| Japonica Intermediate | 241 | 10.00% | 0.00% | 0.41% | 89.63% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 1.04% | 97.92% | NA |
| Intermediate | 90 | 11.10% | 0.00% | 0.00% | 88.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0607893786 | T -> TC | LOC_Os06g14150.1 | splice_region_variant&intron_variant ; LOW | N | Average:6.831; most accessible tissue: Callus, score: 21.877 | N | N | N | N |
| vg0607893786 | T -> TC | LOC_Os06g14140.1 | upstream_gene_variant ; 4049.0bp to feature; MODIFIER | N | Average:6.831; most accessible tissue: Callus, score: 21.877 | N | N | N | N |
| vg0607893786 | T -> TC | LOC_Os06g14160.1 | downstream_gene_variant ; 2692.0bp to feature; MODIFIER | N | Average:6.831; most accessible tissue: Callus, score: 21.877 | N | N | N | N |
| vg0607893786 | T -> DEL | N | N | silent_mutation | Average:6.831; most accessible tissue: Callus, score: 21.877 | N | N | N | N |
| vg0607893786 | T -> C | LOC_Os06g14140.1 | upstream_gene_variant ; 4048.0bp to feature; MODIFIER | silent_mutation | Average:6.831; most accessible tissue: Callus, score: 21.877 | N | N | N | N |
| vg0607893786 | T -> C | LOC_Os06g14160.1 | downstream_gene_variant ; 2693.0bp to feature; MODIFIER | silent_mutation | Average:6.831; most accessible tissue: Callus, score: 21.877 | N | N | N | N |
| vg0607893786 | T -> C | LOC_Os06g14150.1 | intron_variant ; MODIFIER | silent_mutation | Average:6.831; most accessible tissue: Callus, score: 21.877 | N | N | N | N |