| Variant ID: vg1201715501 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr12 | Position: 1715501 |
| Reference Allele: G | Alternative Allele: GTGGT,T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TCCGTCGAGGGGTGTACCAGGGAGAGGTGTACTGGGCTGGCCGAGTGATCAGGCCTCGTCCTTCGCCCATGCTAGGACGACGTCGCCGCGCCGCCGACGG[G/GTGGT,T]
GATGCCCCGATGCAAGATGTCGCGAGATGTCCTCCTGGGCCTCGCGCTGACGAAGGCGTGCGACGCGAGGCAGGAGGAGTGCGCCGTGTGCCTCAGGGAC
GTCCCTGAGGCACACGGCGCACTCCTCCTGCCTCGCGTCGCACGCCTTCGTCAGCGCGAGGCCCAGGAGGACATCTCGCGACATCTTGCATCGGGGCATC[C/ACCAC,A]
CCGTCGGCGGCGCGGCGACGTCGTCCTAGCATGGGCGAAGGACGAGGCCTGATCACTCGGCCAGCCCAGTACACCTCTCCCTGGTACACCCCTCGACGGA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 43.50% | 1.40% | 2.88% | 50.95% | GTGGT: 1.23% |
| All Indica | 2759 | 7.70% | 2.40% | 4.71% | 83.07% | GTGGT: 2.07% |
| All Japonica | 1512 | 97.20% | 0.10% | 0.00% | 2.78% | NA |
| Aus | 269 | 82.20% | 0.00% | 0.37% | 17.47% | NA |
| Indica I | 595 | 1.30% | 0.80% | 4.71% | 92.27% | GTGGT: 0.84% |
| Indica II | 465 | 4.30% | 2.20% | 5.16% | 86.67% | GTGGT: 1.72% |
| Indica III | 913 | 9.60% | 3.70% | 3.40% | 79.96% | GTGGT: 3.29% |
| Indica Intermediate | 786 | 12.30% | 2.30% | 5.98% | 77.61% | GTGGT: 1.78% |
| Temperate Japonica | 767 | 95.40% | 0.10% | 0.00% | 4.43% | NA |
| Tropical Japonica | 504 | 98.80% | 0.00% | 0.00% | 1.19% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 96.90% | 0.00% | 0.00% | 3.12% | NA |
| Intermediate | 90 | 66.70% | 0.00% | 5.56% | 26.67% | GTGGT: 1.11% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1201715501 | G -> DEL | LOC_Os12g04090.1 | N | frameshift_variant | Average:70.728; most accessible tissue: Callus, score: 91.31 | N | N | N | N |
| vg1201715501 | G -> T | LOC_Os12g04090.1 | missense_variant ; p.Gly109Val; MODERATE | nonsynonymous_codon ; G109V | Average:70.728; most accessible tissue: Callus, score: 91.31 | unknown | unknown | TOLERATED | 0.10 |
| vg1201715501 | G -> GTGGT | LOC_Os12g04090.1 | frameshift_variant ; p.Met110fs; HIGH | frameshift_variant | Average:70.728; most accessible tissue: Callus, score: 91.31 | N | N | N | N |