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Detailed information for vg1001933300:
| Variant ID: vg1001933300 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 1933300 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ACCATCTTTGGATGGTCCTTTTGGTCGGTCGCTAGCATCTTGAAAAGGTAGCTGTACTCCTCCTGTGATAAACTATTTAGATGAACTGCCTTTGCTGTTC[C/G]
GAACCTTGCAAGATTTTCAATCCTACTTATGATTACCACTTTGCTTCCTCCAGCTGTCATCTGACTTACAGTAGAATAGAAGTTTACCCAATCATTTTCA
Reverse complement sequence
TGAAAATGATTGGGTAAACTTCTATTCTACTGTAAGTCAGATGACAGCTGGAGGAAGCAAAGTGGTAATCATAAGTAGGATTGAAAATCTTGCAAGGTTC[G/C]
GAACAGCAAAGGCAGTTCATCTAAATAGTTTATCACAGGAGGAGTACAGCTACCTTTTCAAGATGCTAGCGACCGACCAAAAGGACCATCCAAAGATGGT
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 84.70% | 0.20% | 0.36% | 14.79% | NA |
| All Indica | 2759 | 78.00% | 0.00% | 0.40% | 21.57% | NA |
| All Japonica | 1512 | 99.00% | 0.50% | 0.00% | 0.46% | NA |
| Aus | 269 | 65.40% | 0.00% | 2.23% | 32.34% | NA |
| Indica I | 595 | 60.70% | 0.00% | 0.50% | 38.82% | NA |
| Indica II | 465 | 85.60% | 0.00% | 0.22% | 14.19% | NA |
| Indica III | 913 | 80.70% | 0.00% | 0.00% | 19.28% | NA |
| Indica Intermediate | 786 | 83.60% | 0.00% | 0.89% | 15.52% | NA |
| Temperate Japonica | 767 | 98.70% | 0.70% | 0.00% | 0.65% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.90% | 1.20% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 93.30% | 0.00% | 0.00% | 6.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1001933300 | C -> G | LOC_Os10g04160.1 | missense_variant ; p.Gly195Arg; MODERATE | nonsynonymous_codon ; G195R | Average:41.288; most accessible tissue: Callus, score: 77.054 | probably damaging  |
2.64 |
DELETERIOUS | 0.00 |
| vg1001933300 | C -> DEL | LOC_Os10g04160.1 | N | frameshift_variant | Average:41.288; most accessible tissue: Callus, score: 77.054 | N | N | N | N |