Search for Variation information by Variation ID:
Detailed information for vg0112723623:
| Variant ID: vg0112723623 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 12723623 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AGGCCAGCCGTGTAGGCGGAGGCACCACTCGGCGGCGACGGAGGCAGGCCGGCGGTGTAGATGACGATGCCCATCAACGGTGGTGTGACCAACCGACCGT[G/A]
TAGGCGGGGACACCAGTCGGCGGCGACAGAGGCAGGCCGGCGGTGAAGTCGTAGACGCCCAACGGCGGTGGTGTGACCAACCAACCATATAGGCGAAGAC
Reverse complement sequence
GTCTTCGCCTATATGGTTGGTTGGTCACACCACCGCCGTTGGGCGTCTACGACTTCACCGCCGGCCTGCCTCTGTCGCCGCCGACTGGTGTCCCCGCCTA[C/T]
ACGGTCGGTTGGTCACACCACCGTTGATGGGCATCGTCATCTACACCGCCGGCCTGCCTCCGTCGCCGCCGAGTGGTGCCTCCGCCTACACGGCTGGCCT
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 31.20% | 0.40% | 28.37% | 39.97% | NA |
| All Indica | 2759 | 2.60% | 0.00% | 36.61% | 60.75% | NA |
| All Japonica | 1512 | 85.70% | 1.40% | 9.39% | 3.51% | NA |
| Aus | 269 | 2.20% | 0.00% | 49.07% | 48.70% | NA |
| Indica I | 595 | 1.70% | 0.00% | 15.97% | 82.35% | NA |
| Indica II | 465 | 4.10% | 0.00% | 24.52% | 71.40% | NA |
| Indica III | 913 | 1.40% | 0.00% | 59.91% | 38.66% | NA |
| Indica Intermediate | 786 | 3.90% | 0.00% | 32.32% | 63.74% | NA |
| Temperate Japonica | 767 | 94.90% | 0.00% | 2.87% | 2.22% | NA |
| Tropical Japonica | 504 | 73.60% | 4.20% | 16.27% | 5.95% | NA |
| Japonica Intermediate | 241 | 81.70% | 0.00% | 15.77% | 2.49% | NA |
| VI/Aromatic | 96 | 56.20% | 0.00% | 39.58% | 4.17% | NA |
| Intermediate | 90 | 51.10% | 0.00% | 21.11% | 27.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0112723623 | G -> A | LOC_Os01g22620.1 | missense_variant ; p.Thr269Ile; MODERATE | nonsynonymous_codon ; T269I | Average:19.111; most accessible tissue: Minghui63 panicle, score: 50.413 | benign  |
-0.149 |
TOLERATED | 0.32 |
| vg0112723623 | G -> DEL | LOC_Os01g22620.1 | N | frameshift_variant | Average:19.111; most accessible tissue: Minghui63 panicle, score: 50.413 | N | N | N | N |