Search for Variation information by Variation ID:
Detailed information for vg1105974446:
| Variant ID: vg1105974446 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5974446 |
| Reference Allele: T | Alternative Allele: G,C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CGGCAGCTCGGTGACGGCGAAGGGCCGCATCGACATGGACGCCGGGGAGCGCGAGTCGGTGGTGATCGGCGGCACGGGGCGGTTTCGGCTCGCGCGCGGG[T/G,C]
ACATGGTCACCAAGAACTACGACTACAGCCTCGCCACCGGCGGCGTCGTCCAGATCGACGTCTGCCTGCAGCACTAGCTAGCCATGGACAGAAAACGCAC
Reverse complement sequence
GTGCGTTTTCTGTCCATGGCTAGCTAGTGCTGCAGGCAGACGTCGATCTGGACGACGCCGCCGGTGGCGAGGCTGTAGTCGTAGTTCTTGGTGACCATGT[A/C,G]
CCCGCGCGCGAGCCGAAACCGCCCCGTGCCGCCGATCACCACCGACTCGCGCTCCCCGGCGTCCATGTCGATGCGGCCCTTCGCCGTCACCGAGCTGCCG
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 | 51.20% | 0.40% | 1.74% | 46.61% | NA |
| All Indica | 2759 | 35.00% | 0.50% | 2.32% | 62.23% | NA |
| All Japonica | 1512 | 83.30% | 0.30% | 0.86% | 15.48% | NA |
| Aus | 269 | 19.70% | 0.00% | 1.49% | 78.81% | NA |
| Indica I | 595 | 40.20% | 0.30% | 3.03% | 56.47% | NA |
| Indica II | 465 | 28.40% | 0.00% | 2.37% | 69.25% | NA |
| Indica III | 913 | 32.10% | 0.20% | 1.53% | 66.16% | NA |
| Indica Intermediate | 786 | 38.30% | 1.10% | 2.67% | 57.89% | NA |
| Temperate Japonica | 767 | 73.70% | 0.00% | 1.30% | 25.03% | NA |
| Tropical Japonica | 504 | 95.40% | 1.00% | 0.20% | 3.37% | NA |
| Japonica Intermediate | 241 | 88.80% | 0.00% | 0.83% | 10.37% | NA |
| VI/Aromatic | 96 | 88.50% | 0.00% | 1.04% | 10.42% | NA |
| Intermediate | 90 | 65.60% | 1.10% | 0.00% | 33.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105974446 | T -> DEL | LOC_Os11g10840.1 | N | frameshift_variant | Average:33.73; most accessible tissue: Callus, score: 75.127 | N | N | N | N |
| vg1105974446 | T -> G | LOC_Os11g10840.1 | missense_variant ; p.Tyr43Asp; MODERATE | N | Average:33.73; most accessible tissue: Callus, score: 75.127 | N | N | N | N |
| vg1105974446 | T -> G | LOC_Os11g10830.1 | upstream_gene_variant ; 1608.0bp to feature; MODIFIER | N | Average:33.73; most accessible tissue: Callus, score: 75.127 | N | N | N | N |
| vg1105974446 | T -> G | LOC_Os11g10850.1 | upstream_gene_variant ; 3971.0bp to feature; MODIFIER | N | Average:33.73; most accessible tissue: Callus, score: 75.127 | N | N | N | N |
| vg1105974446 | T -> G | LOC_Os11g10820.1 | downstream_gene_variant ; 4865.0bp to feature; MODIFIER | N | Average:33.73; most accessible tissue: Callus, score: 75.127 | N | N | N | N |
| vg1105974446 | T -> C | LOC_Os11g10840.1 | missense_variant ; p.Tyr43His; MODERATE | nonsynonymous_codon ; Y43H | Average:33.73; most accessible tissue: Callus, score: 75.127 | probably damaging  |
2.234 |
DELETERIOUS | 0.00 |