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Detailed information for vg1001933010:
| Variant ID: vg1001933010 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr10 | Position: 1933010 |
| Reference Allele: CTG | Alternative Allele: GTG,TTG,C |
| Primary Allele: CTG | Secondary Allele: GTG |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TCTTATAGTTTGGAATATCATCCCTTTCTACTCGAGGTGGCTTTACAAGAATGCAGGCGTGAGTAGGATAAGATGTCATAAATTCGGTGCTATCTACTGG[CTG/GTG,TTG,C]
CTCTTTCTCAATGATATCTTTCGGATGCTCACCATATTTCAAAAAGTTGTTCTTCACCATCCTCTCGAAGCGTCGCAATATTCTAAGCCAGAAGTGAACA
Reverse complement sequence
TGTTCACTTCTGGCTTAGAATATTGCGACGCTTCGAGAGGATGGTGAAGAACAACTTTTTGAAATATGGTGAGCATCCGAAAGATATCATTGAGAAAGAG[CAG/CAC,CAA,G]
CCAGTAGATAGCACCGAATTTATGACATCTTATCCTACTCACGCCTGCATTCTTGTAAAGCCACCTCGAGTAGAAAGGGATGATATTCCAAACTATAAGA
Allele Frequencies:
| Populations | Population Size | Frequency of CTG(primary allele) | Frequency of GTG(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 43.00% | 32.60% | 0.55% | 16.10% | TTG: 7.74%; C: 0.02% |
| All Indica | 2759 | 18.30% | 53.40% | 0.87% | 23.16% | TTG: 4.28% |
| All Japonica | 1512 | 90.50% | 3.00% | 0.00% | 0.60% | TTG: 5.89%; C: 0.07% |
| Aus | 269 | 3.70% | 1.50% | 0.74% | 38.29% | TTG: 55.76% |
| Indica I | 595 | 3.50% | 53.90% | 1.68% | 40.67% | TTG: 0.17% |
| Indica II | 465 | 20.00% | 63.70% | 0.43% | 15.70% | TTG: 0.22% |
| Indica III | 913 | 27.20% | 47.40% | 0.22% | 20.26% | TTG: 4.93% |
| Indica Intermediate | 786 | 18.10% | 53.90% | 1.27% | 17.68% | TTG: 9.03% |
| Temperate Japonica | 767 | 96.70% | 0.50% | 0.00% | 0.91% | TTG: 1.83% |
| Tropical Japonica | 504 | 80.00% | 7.10% | 0.00% | 0.00% | TTG: 12.70%; C: 0.20% |
| Japonica Intermediate | 241 | 92.50% | 2.10% | 0.00% | 0.83% | TTG: 4.56% |
| VI/Aromatic | 96 | 92.70% | 0.00% | 0.00% | 4.17% | TTG: 3.12% |
| Intermediate | 90 | 67.80% | 18.90% | 0.00% | 6.67% | TTG: 6.67% |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1001933010 | CTG -> C | LOC_Os10g04160.1 | frameshift_variant ; p.Gln291fs; HIGH | frameshift_variant | Average:36.773; most accessible tissue: Callus, score: 73.936 | N | N | N | N |
| vg1001933010 | CTG -> TTG | LOC_Os10g04160.1 | synonymous_variant ; p.Gln291Gln; LOW | synonymous_codon | Average:36.773; most accessible tissue: Callus, score: 73.936 | N | N | N | N |
| vg1001933010 | CTG -> GTG | LOC_Os10g04160.1 | missense_variant ; p.Gln291His; MODERATE | nonsynonymous_codon ; Q291H | Average:36.773; most accessible tissue: Callus, score: 73.936 | possibly damaging  |
+1.680 |
N | N |
| vg1001933010 | CTG -> DEL | LOC_Os10g04160.1 | N | frameshift_variant | Average:36.773; most accessible tissue: Callus, score: 73.936 | N | N | N | N |