Search for Variation information by Variation ID:
Detailed information for vg1105160999:
| Variant ID: vg1105160999 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5160999 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GTCGCCGTAGACGAGGAGGCGACGCTCCCCACCTCGCCGCCCTTCCCCATCACCCGTGGATGTCGAAGTCGCGGATCCTTCGACCCTCTCGAGCGCCTCC[T/C]
CCCGCCTAGGACTTTGGCGTGGAGGGGGCGGTGGAGTACGAGCTCGACGGCGTGGGTTTGGCTCCCCGTCGTCACCGCTAACACTCGGAGAGAGGTTGTG
Reverse complement sequence
CACAACCTCTCTCCGAGTGTTAGCGGTGACGACGGGGAGCCAAACCCACGCCGTCGAGCTCGTACTCCACCGCCCCCTCCACGCCAAAGTCCTAGGCGGG[A/G]
GGAGGCGCTCGAGAGGGTCGAAGGATCCGCGACTTCGACATCCACGGGTGATGGGGAAGGGCGGCGAGGTGGGGAGCGTCGCCTCCTCGTCTACGGCGAC
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 48.90% | 0.30% | 18.62% | 32.16% | NA |
| All Indica | 2759 | 28.30% | 0.50% | 27.11% | 44.07% | NA |
| All Japonica | 1512 | 90.10% | 0.00% | 1.59% | 8.33% | NA |
| Aus | 269 | 18.60% | 0.70% | 32.71% | 47.96% | NA |
| Indica I | 595 | 18.50% | 0.00% | 14.29% | 67.23% | NA |
| Indica II | 465 | 17.80% | 0.40% | 27.53% | 54.19% | NA |
| Indica III | 913 | 36.30% | 0.70% | 39.10% | 23.99% | NA |
| Indica Intermediate | 786 | 32.70% | 0.80% | 22.65% | 43.89% | NA |
| Temperate Japonica | 767 | 90.10% | 0.00% | 0.91% | 9.00% | NA |
| Tropical Japonica | 504 | 94.00% | 0.00% | 0.79% | 5.16% | NA |
| Japonica Intermediate | 241 | 81.70% | 0.00% | 5.39% | 12.86% | NA |
| VI/Aromatic | 96 | 69.80% | 0.00% | 9.38% | 20.83% | NA |
| Intermediate | 90 | 55.60% | 0.00% | 12.22% | 32.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105160999 | T -> DEL | LOC_Os11g09660.1 | N | frameshift_variant | Average:6.767; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg1105160999 | T -> C | LOC_Os11g09660.1 | missense_variant ; p.Glu41Gly; MODERATE | nonsynonymous_codon ; E41G | Average:6.767; most accessible tissue: Zhenshan97 panicle, score: 16.188 | possibly damaging  |
1.636 |
TOLERATED | 0.53 |