| Variant ID: vg1105182729 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 5182729 |
| Reference Allele: TGAGCTA | Alternative Allele: T |
| Primary Allele: TGAGCTA | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TTTTCATTGGTACTTTTTCTTTTTTTAGATCTGAAATGTCCTCGAGTGAAGGATCTAAGTGGGTTTCGCGATGTGTCTTTGGCTCCCCTCCGAATCTTTC[TGAGCTA/T]
GATGAGTTGGCGGTTCTTTATCATGAACAAGCTGCAAGGAACACTAGAGACTACGTTAGAAGCTGGATCTGCCCCGACTGTAGGAAGGAGTACAAGCCTA
TAGGCTTGTACTCCTTCCTACAGTCGGGGCAGATCCAGCTTCTAACGTAGTCTCTAGTGTTCCTTGCAGCTTGTTCATGATAAAGAACCGCCAACTCATC[TAGCTCA/A]
GAAAGATTCGGAGGGGAGCCAAAGACACATCGCGAAACCCACTTAGATCCTTCACTCGAGGACATTTCAGATCTAAAAAAAGAAAAAGTACCAATGAAAA
| Populations | Population Size | Frequency of TGAGCTA(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 64.40% | 4.10% | 0.74% | 30.79% | NA |
| All Indica | 2759 | 49.70% | 1.50% | 1.05% | 47.81% | NA |
| All Japonica | 1512 | 97.50% | 1.20% | 0.13% | 1.19% | NA |
| Aus | 269 | 22.70% | 44.60% | 0.74% | 31.97% | NA |
| Indica I | 595 | 29.20% | 0.30% | 1.85% | 68.57% | NA |
| Indica II | 465 | 22.80% | 0.00% | 0.65% | 76.56% | NA |
| Indica III | 913 | 71.50% | 1.50% | 0.55% | 26.40% | NA |
| Indica Intermediate | 786 | 55.60% | 3.20% | 1.27% | 39.95% | NA |
| Temperate Japonica | 767 | 97.70% | 0.00% | 0.26% | 2.09% | NA |
| Tropical Japonica | 504 | 96.80% | 3.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.80% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 78.10% | 13.50% | 0.00% | 8.33% | NA |
| Intermediate | 90 | 68.90% | 2.20% | 2.22% | 26.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105182729 | TGAGCTA -> T | LOC_Os11g09710.1 | disruptive_inframe_deletion ; p.Glu23_Leu24del; MODERATE | inframe_variant | Average:13.899; most accessible tissue: Callus, score: 85.245 | N | N | N | N |
| vg1105182729 | TGAGCTA -> DEL | LOC_Os11g09710.1 | N | frameshift_variant | Average:13.899; most accessible tissue: Callus, score: 85.245 | N | N | N | N |