| Variant ID: vg1001933511 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr10 | Position: 1933511 |
| Reference Allele: GTATGAT | Alternative Allele: CTATGAT,G |
| Primary Allele: GTATGAT | Secondary Allele: CTATGAT |
Inferred Ancestral Allele: Not determined.
TAAAATATTCACGAACAATCAATGTCCTCTCCATTTTGAACTTTGCATGTGCTATTGATCCGCAGCTGCTATCTCCATTGATGTACAAAATAGAAGAAAA[GTATGAT/CTATGAT,G]
CTGATCCGCTCATCATTGCAGACATGGCTGATCAAGGATTTCTTTCCTACCCTGCAACCACCAATGATTGGAAGAACAAGACGAGCACCCTGGTTACCTG
CAGGTAACCAGGGTGCTCGTCTTGTTCTTCCAATCATTGGTGGTTGCAGGGTAGGAAAGAAATCCTTGATCAGCCATGTCTGCAATGATGAGCGGATCAG[ATCATAC/ATCATAG,C]
TTTTCTTCTATTTTGTACATCAATGGAGATAGCAGCTGCGGATCAATAGCACATGCAAAGTTCAAAATGGAGAGGACATTGATTGTTCGTGAATATTTTA
| Populations | Population Size | Frequency of GTATGAT(primary allele) | Frequency of CTATGAT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 81.40% | 3.40% | 0.44% | 14.77% | G: 0.02% |
| All Indica | 2759 | 72.40% | 5.60% | 0.47% | 21.53% | G: 0.04% |
| All Japonica | 1512 | 99.50% | 0.00% | 0.07% | 0.40% | NA |
| Aus | 269 | 64.30% | 0.00% | 1.49% | 34.20% | NA |
| Indica I | 595 | 60.70% | 0.00% | 0.67% | 38.49% | G: 0.17% |
| Indica II | 465 | 81.90% | 3.40% | 0.22% | 14.41% | NA |
| Indica III | 913 | 70.50% | 10.10% | 0.66% | 18.73% | NA |
| Indica Intermediate | 786 | 77.70% | 5.90% | 0.25% | 16.16% | NA |
| Temperate Japonica | 767 | 99.30% | 0.00% | 0.13% | 0.52% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 96.90% | 0.00% | 3.12% | 0.00% | NA |
| Intermediate | 90 | 85.60% | 7.80% | 0.00% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1001933511 | GTATGAT -> CTATGAT | LOC_Os10g04160.1 | stop_gained ; p.Tyr124*; HIGH | stop_gained | Average:39.167; most accessible tissue: Callus, score: 75.859 | N | N | N | N |
| vg1001933511 | GTATGAT -> G | LOC_Os10g04160.1 | disruptive_inframe_deletion ; p.Arg122_Tyr124delinsSer; MODERATE | inframe_variant | Average:39.167; most accessible tissue: Callus, score: 75.859 | N | N | N | N |
| vg1001933511 | GTATGAT -> DEL | LOC_Os10g04160.1 | N | frameshift_variant | Average:39.167; most accessible tissue: Callus, score: 75.859 | N | N | N | N |