| Variant ID: vg0334098434 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr03 | Position: 34098434 |
| Reference Allele: C | Alternative Allele: CTTG |
| Primary Allele: CTTG | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CTGTGAGGTAAATTTTGTTTAATTCGTTTGTGTTCTCATTATGAACAGTTCCGTATTAGTTCAATACTTTCCTGATATAACTAATCATAACTATTATCTT[C/CTTG]
TTGCAGCCGAAGTGGGTTAGCGGGACGACGCGTCGTGTGTACACACAGTTCGTAGCTGATTTTGATCAGCTTACGTCTAACCGTGTTCGGTGGACTCCCT
AGGGAGTCCACCGAACACGGTTAGACGTAAGCTGATCAAAATCAGCTACGAACTGTGTGTACACACGACGCGTCGTCCCGCTAACCCACTTCGGCTGCAA[G/CAAG]
AAGATAATAGTTATGATTAGTTATATCAGGAAAGTATTGAACTAATACGGAACTGTTCATAATGAGAACACAAACGAATTAAACAAAATTTACCTCACAG
| Populations | Population Size | Frequency of CTTG(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 54.00% | 45.30% | 0.19% | 0.47% | NA |
| All Indica | 2759 | 81.90% | 17.10% | 0.33% | 0.69% | NA |
| All Japonica | 1512 | 2.20% | 97.80% | 0.00% | 0.00% | NA |
| Aus | 269 | 79.60% | 20.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 86.60% | 12.80% | 0.17% | 0.50% | NA |
| Indica II | 465 | 93.50% | 5.80% | 0.43% | 0.22% | NA |
| Indica III | 913 | 71.40% | 27.80% | 0.11% | 0.66% | NA |
| Indica Intermediate | 786 | 83.70% | 14.50% | 0.64% | 1.15% | NA |
| Temperate Japonica | 767 | 0.70% | 99.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 5.40% | 94.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 0.80% | 99.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 5.20% | 93.80% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 45.60% | 52.20% | 0.00% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0334098434 | C -> CTTG | LOC_Os03g59910.1 | splice_region_variant&intron_variant ; LOW | silent_mutation | Average:51.479; most accessible tissue: Callus, score: 68.635 | N | N | N | N |
| vg0334098434 | C -> CTTG | LOC_Os03g59894.1 | downstream_gene_variant ; 1768.0bp to feature; MODIFIER | silent_mutation | Average:51.479; most accessible tissue: Callus, score: 68.635 | N | N | N | N |
| vg0334098434 | C -> CTTG | LOC_Os03g59920.1 | downstream_gene_variant ; 1126.0bp to feature; MODIFIER | silent_mutation | Average:51.479; most accessible tissue: Callus, score: 68.635 | N | N | N | N |
| vg0334098434 | C -> DEL | N | N | silent_mutation | Average:51.479; most accessible tissue: Callus, score: 68.635 | N | N | N | N |