| Variant ID: vg0521975533 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr05 | Position: 21975533 |
| Reference Allele: GT | Alternative Allele: G |
| Primary Allele: GT | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
AGGATGGATAAACAAGTGAAGAACCACAGACCTTCTGATGGTACGGATGGATCAAGGTATGTTGTTCTGTTTCAGTGATTTATTTCAGTATGTGCCGCTG[GT/G]
TTTTTTTCTCTGAATTTCGCCGTGTGAACTTGAGCAATTCTAAATCATCAATTCAGGGAAATTCTTATGGACGAGCGCAACCCTACCATGGACATAGTAG
CTACTATGTCCATGGTAGGGTTGCGCTCGTCCATAAGAATTTCCCTGAATTGATGATTTAGAATTGCTCAAGTTCACACGGCGAAATTCAGAGAAAAAAA[AC/C]
CAGCGGCACATACTGAAATAAATCACTGAAACAGAACAACATACCTTGATCCATCCGTACCATCAGAAGGTCTGTGGTTCTTCACTTGTTTATCCATCCT
| Populations | Population Size | Frequency of GT(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 39.30% | 0.10% | 6.22% | 54.40% | NA |
| All Indica | 2759 | 3.50% | 0.10% | 9.82% | 86.52% | NA |
| All Japonica | 1512 | 98.80% | 0.10% | 0.26% | 0.86% | NA |
| Aus | 269 | 45.00% | 0.00% | 5.58% | 49.44% | NA |
| Indica I | 595 | 2.50% | 0.00% | 12.77% | 84.71% | NA |
| Indica II | 465 | 5.60% | 0.40% | 5.16% | 88.82% | NA |
| Indica III | 913 | 1.20% | 0.00% | 12.81% | 85.98% | NA |
| Indica Intermediate | 786 | 5.70% | 0.30% | 6.87% | 87.15% | NA |
| Temperate Japonica | 767 | 98.80% | 0.00% | 0.13% | 1.04% | NA |
| Tropical Japonica | 504 | 99.20% | 0.20% | 0.20% | 0.40% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.00% | 0.83% | 1.24% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 55.60% | 0.00% | 4.44% | 40.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0521975533 | GT -> DEL | N | N | silent_mutation | Average:6.787; most accessible tissue: Callus, score: 29.988 | N | N | N | N |
| vg0521975533 | GT -> G | LOC_Os05g37530.1 | downstream_gene_variant ; 4351.0bp to feature; MODIFIER | silent_mutation | Average:6.787; most accessible tissue: Callus, score: 29.988 | N | N | N | N |
| vg0521975533 | GT -> G | LOC_Os05g37550.1 | downstream_gene_variant ; 4553.0bp to feature; MODIFIER | silent_mutation | Average:6.787; most accessible tissue: Callus, score: 29.988 | N | N | N | N |
| vg0521975533 | GT -> G | LOC_Os05g37540.1 | intron_variant ; MODIFIER | silent_mutation | Average:6.787; most accessible tissue: Callus, score: 29.988 | N | N | N | N |