Search for Variation information by Variation ID:
Detailed information for vg1105974381:
| Variant ID: vg1105974381 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5974381 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TCTTTTTTCGACAGCGTGGTGTCGGACCTGAGCCTGCACATGGTGCTGGAGGCCGGCGAGCACCGCGGCAGCTCGGTGACGGCGAAGGGCCGCATCGACA[T/C]
GGACGCCGGGGAGCGCGAGTCGGTGGTGATCGGCGGCACGGGGCGGTTTCGGCTCGCGCGCGGGTACATGGTCACCAAGAACTACGACTACAGCCTCGCC
Reverse complement sequence
GGCGAGGCTGTAGTCGTAGTTCTTGGTGACCATGTACCCGCGCGCGAGCCGAAACCGCCCCGTGCCGCCGATCACCACCGACTCGCGCTCCCCGGCGTCC[A/G]
TGTCGATGCGGCCCTTCGCCGTCACCGAGCTGCCGCGGTGCTCGCCGGCCTCCAGCACCATGTGCAGGCTCAGGTCCGACACCACGCTGTCGAAAAAAGA
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 | 91.00% | 0.40% | 4.23% | 4.32% | NA |
| All Indica | 2759 | 91.60% | 0.50% | 5.26% | 2.68% | NA |
| All Japonica | 1512 | 88.50% | 0.30% | 3.17% | 8.00% | NA |
| Aus | 269 | 96.30% | 0.00% | 1.49% | 2.23% | NA |
| Indica I | 595 | 88.10% | 0.30% | 7.90% | 3.70% | NA |
| Indica II | 465 | 91.20% | 0.00% | 6.02% | 2.80% | NA |
| Indica III | 913 | 95.10% | 0.20% | 3.18% | 1.53% | NA |
| Indica Intermediate | 786 | 90.50% | 1.10% | 5.22% | 3.18% | NA |
| Temperate Japonica | 767 | 81.10% | 0.00% | 5.48% | 13.43% | NA |
| Tropical Japonica | 504 | 98.20% | 1.00% | 0.20% | 0.60% | NA |
| Japonica Intermediate | 241 | 91.70% | 0.00% | 2.07% | 6.22% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 1.04% | 1.04% | NA |
| Intermediate | 90 | 94.40% | 1.10% | 2.22% | 2.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105974381 | T -> DEL | LOC_Os11g10840.1 | N | frameshift_variant | Average:24.362; most accessible tissue: Callus, score: 34.526 | N | N | N | N |
| vg1105974381 | T -> C | LOC_Os11g10840.1 | missense_variant ; p.Met21Thr; MODERATE | nonsynonymous_codon ; M21T | Average:24.362; most accessible tissue: Callus, score: 34.526 | benign  |
-0.013 |
TOLERATED | 0.16 |