Search for Variation information by Variation ID:
Detailed information for vg0100791512:
| Variant ID: vg0100791512 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 791512 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AAGATATAATGAAGAGATACATTTGAAGGTCGAAATGTTTCTCAAGACATATGGCACATCGAAACCCACAAGGTATAGTTTCTCTGAAGTTAAGAAGATT[A/T]
CAAGACGGTTCAGGGAAAAGATAGGCCACGGTGGGTATGGAAATGTATACAAGGGTGAGCTACCAAATGGAGTGCCCGTGGCAGTTAAGATGCTAGAAAA
Reverse complement sequence
TTTTCTAGCATCTTAACTGCCACGGGCACTCCATTTGGTAGCTCACCCTTGTATACATTTCCATACCCACCGTGGCCTATCTTTTCCCTGAACCGTCTTG[T/A]
AATCTTCTTAACTTCAGAGAAACTATACCTTGTGGGTTTCGATGTGCCATATGTCTTGAGAAACATTTCGACCTTCAAATGTATCTCTTCATTATATCTT
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 55.80% | 1.40% | 1.84% | 40.90% | NA |
| All Indica | 2759 | 49.70% | 1.20% | 2.65% | 46.43% | NA |
| All Japonica | 1512 | 72.50% | 1.10% | 0.46% | 25.93% | NA |
| Aus | 269 | 36.10% | 5.20% | 1.12% | 57.62% | NA |
| Indica I | 595 | 68.90% | 0.50% | 0.67% | 29.92% | NA |
| Indica II | 465 | 75.70% | 0.00% | 1.08% | 23.23% | NA |
| Indica III | 913 | 18.00% | 2.80% | 3.50% | 75.68% | NA |
| Indica Intermediate | 786 | 56.60% | 0.60% | 4.07% | 38.68% | NA |
| Temperate Japonica | 767 | 69.60% | 1.40% | 0.52% | 28.42% | NA |
| Tropical Japonica | 504 | 82.90% | 0.40% | 0.20% | 16.47% | NA |
| Japonica Intermediate | 241 | 59.80% | 1.70% | 0.83% | 37.76% | NA |
| VI/Aromatic | 96 | 10.40% | 2.10% | 2.08% | 85.42% | NA |
| Intermediate | 90 | 71.10% | 1.10% | 2.22% | 25.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0100791512 | A -> T | LOC_Os01g02440.1 | missense_variant ; p.Thr263Ser; MODERATE | nonsynonymous_codon ; T263S | Average:52.739; most accessible tissue: Zhenshan97 panicle, score: 67.02 | benign  |
0.645 |
DELETERIOUS | 0.03 |
| vg0100791512 | A -> DEL | LOC_Os01g02440.1 | N | frameshift_variant | Average:52.739; most accessible tissue: Zhenshan97 panicle, score: 67.02 | N | N | N | N |