Search for Variation information by Variation ID:
Detailed information for vg1126362959:
| Variant ID: vg1126362959 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 26362959 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CTCCCTCCACGATCTTGCGGACTGTCGCGCAGTCAAAAACTTGGCTGAGCGAACGAGGAAGTGGGAGGAGGACAGGAGGCAGGAACGCCGTGAGGGCAAG[T/A]
CTGCGGCAGTTCCCTCCGGTAAACGGCGAAGTGAGGCCAGACAGAAGGCCCCCGCCGTTGACATCGATGATGGTGATGATGACCTAGGTTTCCAAGAACC
Reverse complement sequence
GGTTCTTGGAAACCTAGGTCATCATCACCATCATCGATGTCAACGGCGGGGGCCTTCTGTCTGGCCTCACTTCGCCGTTTACCGGAGGGAACTGCCGCAG[A/T]
CTTGCCCTCACGGCGTTCCTGCCTCCTGTCCTCCTCCCACTTCCTCGTTCGCTCAGCCAAGTTTTTGACTGCGCGACAGTCCGCAAGATCGTGGAGGGAG
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 12.20% | 0.20% | 26.75% | 60.83% | NA |
| All Indica | 2759 | 4.20% | 0.00% | 20.99% | 74.77% | NA |
| All Japonica | 1512 | 25.40% | 0.70% | 34.06% | 39.81% | NA |
| Aus | 269 | 21.20% | 0.00% | 38.29% | 40.52% | NA |
| Indica I | 595 | 1.50% | 0.00% | 11.60% | 86.89% | NA |
| Indica II | 465 | 3.00% | 0.00% | 12.90% | 84.09% | NA |
| Indica III | 913 | 4.20% | 0.00% | 31.00% | 64.84% | NA |
| Indica Intermediate | 786 | 7.10% | 0.00% | 21.25% | 71.63% | NA |
| Temperate Japonica | 767 | 37.00% | 1.40% | 13.56% | 47.98% | NA |
| Tropical Japonica | 504 | 7.10% | 0.00% | 62.30% | 30.56% | NA |
| Japonica Intermediate | 241 | 26.60% | 0.00% | 40.25% | 33.20% | NA |
| VI/Aromatic | 96 | 2.10% | 0.00% | 48.96% | 48.96% | NA |
| Intermediate | 90 | 17.80% | 0.00% | 22.22% | 60.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1126362959 | T -> A | LOC_Os11g43670.1 | missense_variant ; p.Ser514Thr; MODERATE | nonsynonymous_codon ; S514T | Average:13.36; most accessible tissue: Minghui63 panicle, score: 20.733 | benign  |
1.429 |
TOLERATED | 0.10 |
| vg1126362959 | T -> DEL | LOC_Os11g43670.1 | N | frameshift_variant | Average:13.36; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |