| Variant ID: vg1201715495 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr12 | Position: 1715495 |
| Reference Allele: C | Alternative Allele: CGGT |
| Primary Allele: C | Secondary Allele: CGGT |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 101. )
AAGAGTTCCGTCGAGGGGTGTACCAGGGAGAGGTGTACTGGGCTGGCCGAGTGATCAGGCCTCGTCCTTCGCCCATGCTAGGACGACGTCGCCGCGCCGC[C/CGGT]
GACGGGGATGCCCCGATGCAAGATGTCGCGAGATGTCCTCCTGGGCCTCGCGCTGACGAAGGCGTGCGACGCGAGGCAGGAGGAGTGCGCCGTGTGCCTC
GAGGCACACGGCGCACTCCTCCTGCCTCGCGTCGCACGCCTTCGTCAGCGCGAGGCCCAGGAGGACATCTCGCGACATCTTGCATCGGGGCATCCCCGTC[G/ACCG]
GCGGCGCGGCGACGTCGTCCTAGCATGGGCGAAGGACGAGGCCTGATCACTCGGCCAGCCCAGTACACCTCTCCCTGGTACACCCCTCGACGGAACTCTT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of CGGT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 45.90% | 6.70% | 11.11% | 36.20% | NA |
| All Indica | 2759 | 11.60% | 11.00% | 17.91% | 59.48% | NA |
| All Japonica | 1512 | 97.40% | 0.30% | 0.60% | 1.72% | NA |
| Aus | 269 | 83.30% | 2.60% | 5.20% | 8.92% | NA |
| Indica I | 595 | 3.00% | 7.10% | 22.52% | 67.39% | NA |
| Indica II | 465 | 8.00% | 9.70% | 19.78% | 62.58% | NA |
| Indica III | 913 | 15.10% | 15.60% | 12.60% | 56.74% | NA |
| Indica Intermediate | 786 | 16.20% | 9.50% | 19.47% | 54.83% | NA |
| Temperate Japonica | 767 | 95.80% | 0.70% | 0.65% | 2.87% | NA |
| Tropical Japonica | 504 | 98.80% | 0.00% | 0.60% | 0.60% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.41% | 0.41% | NA |
| VI/Aromatic | 96 | 96.90% | 1.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 68.90% | 2.20% | 8.89% | 20.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1201715495 | C -> DEL | LOC_Os12g04090.1 | N | frameshift_variant | Average:70.89; most accessible tissue: Callus, score: 91.31 | N | N | N | N |
| vg1201715495 | C -> CGGT | LOC_Os12g04090.1 | inframe_insertion ; p.Pro107_Thr108insVal; MODERATE | inframe_variant | Average:70.89; most accessible tissue: Callus, score: 91.31 | N | N | N | N |