| Variant ID: vg1100674083 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 674083 |
| Reference Allele: CTAAT | Alternative Allele: C |
| Primary Allele: CTAAT | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TCACGTTTCTCAAGTAACTTTTTTATCTATCTGAATATTGTTTATTCATAATTTCATATTTCTAAAATTACCTTCTGTGGTGTTTAGGCCAATACTGCTG[CTAAT/C]
TCTCAAAGTGAAGACTGCTGAACTGTGAATTTCGTAAGAACTTTGAGTCGTATTAAACTATTAATGTATTGATACGCAGCAGATGGGAGATAATCTTCTT
AAGAAGATTATCTCCCATCTGCTGCGTATCAATACATTAATAGTTTAATACGACTCAAAGTTCTTACGAAATTCACAGTTCAGCAGTCTTCACTTTGAGA[ATTAG/G]
CAGCAGTATTGGCCTAAACACCACAGAAGGTAATTTTAGAAATATGAAATTATGAATAAACAATATTCAGATAGATAAAAAAGTTACTTGAGAAACGTGA
| Populations | Population Size | Frequency of CTAAT(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 95.70% | 4.20% | 0.04% | 0.00% | NA |
| All Indica | 2759 | 97.80% | 2.10% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 50.20% | 49.40% | 0.37% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| Indica III | 913 | 97.20% | 2.80% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 96.10% | 3.80% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 94.80% | 5.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 3.30% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1100674083 | CTAAT -> C | LOC_Os11g02310.1 | 3_prime_UTR_variant ; 877.0bp to feature; MODIFIER | silent_mutation | Average:47.794; most accessible tissue: Minghui63 flower, score: 63.841 | N | N | N | N |
| vg1100674083 | CTAAT -> C | LOC_Os11g02320.1 | upstream_gene_variant ; 2383.0bp to feature; MODIFIER | silent_mutation | Average:47.794; most accessible tissue: Minghui63 flower, score: 63.841 | N | N | N | N |
| vg1100674083 | CTAAT -> C | LOC_Os11g02320.2 | upstream_gene_variant ; 2383.0bp to feature; MODIFIER | silent_mutation | Average:47.794; most accessible tissue: Minghui63 flower, score: 63.841 | N | N | N | N |
| vg1100674083 | CTAAT -> C | LOC_Os11g02320.3 | upstream_gene_variant ; 2383.0bp to feature; MODIFIER | silent_mutation | Average:47.794; most accessible tissue: Minghui63 flower, score: 63.841 | N | N | N | N |