Search for Variation information by Variation ID:
Detailed information for vg1105974431:
| Variant ID: vg1105974431 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5974431 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GGCCGGCGAGCACCGCGGCAGCTCGGTGACGGCGAAGGGCCGCATCGACATGGACGCCGGGGAGCGCGAGTCGGTGGTGATCGGCGGCACGGGGCGGTTT[C/T]
GGCTCGCGCGCGGGTACATGGTCACCAAGAACTACGACTACAGCCTCGCCACCGGCGGCGTCGTCCAGATCGACGTCTGCCTGCAGCACTAGCTAGCCAT
Reverse complement sequence
ATGGCTAGCTAGTGCTGCAGGCAGACGTCGATCTGGACGACGCCGCCGGTGGCGAGGCTGTAGTCGTAGTTCTTGGTGACCATGTACCCGCGCGCGAGCC[G/A]
AAACCGCCCCGTGCCGCCGATCACCACCGACTCGCGCTCCCCGGCGTCCATGTCGATGCGGCCCTTCGCCGTCACCGAGCTGCCGCGGTGCTCGCCGGCC
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 38.10% | 2.60% | 10.22% | 49.05% | NA |
| All Indica | 2759 | 29.90% | 0.80% | 10.15% | 59.15% | NA |
| All Japonica | 1512 | 56.70% | 6.60% | 10.38% | 26.32% | NA |
| Aus | 269 | 12.60% | 0.00% | 11.90% | 75.46% | NA |
| Indica I | 595 | 30.90% | 0.00% | 17.31% | 51.76% | NA |
| Indica II | 465 | 22.60% | 0.20% | 11.18% | 66.02% | NA |
| Indica III | 913 | 29.80% | 1.80% | 4.82% | 63.64% | NA |
| Indica Intermediate | 786 | 33.60% | 0.60% | 10.31% | 55.47% | NA |
| Temperate Japonica | 767 | 56.50% | 2.10% | 12.26% | 29.20% | NA |
| Tropical Japonica | 504 | 52.80% | 13.30% | 7.74% | 26.19% | NA |
| Japonica Intermediate | 241 | 65.60% | 7.10% | 9.96% | 17.43% | NA |
| VI/Aromatic | 96 | 39.60% | 0.00% | 6.25% | 54.17% | NA |
| Intermediate | 90 | 51.10% | 3.30% | 8.89% | 36.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105974431 | C -> T | LOC_Os11g10840.1 | missense_variant ; p.Arg38Trp; MODERATE | nonsynonymous_codon ; R38W | Average:33.674; most accessible tissue: Callus, score: 75.127 | probably damaging  |
3.66 |
DELETERIOUS | 0.00 |
| vg1105974431 | C -> DEL | LOC_Os11g10840.1 | N | frameshift_variant | Average:33.674; most accessible tissue: Callus, score: 75.127 | N | N | N | N |