Search for Variation information by Variation ID:
Detailed information for vg0112723630:
| Variant ID: vg0112723630 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 12723630 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CCGTGTAGGCGGAGGCACCACTCGGCGGCGACGGAGGCAGGCCGGCGGTGTAGATGACGATGCCCATCAACGGTGGTGTGACCAACCGACCGTGTAGGCG[G/A]
GGACACCAGTCGGCGGCGACAGAGGCAGGCCGGCGGTGAAGTCGTAGACGCCCAACGGCGGTGGTGTGACCAACCAACCATATAGGCGAAGACACCAGTC
Reverse complement sequence
GACTGGTGTCTTCGCCTATATGGTTGGTTGGTCACACCACCGCCGTTGGGCGTCTACGACTTCACCGCCGGCCTGCCTCTGTCGCCGCCGACTGGTGTCC[C/T]
CGCCTACACGGTCGGTTGGTCACACCACCGTTGATGGGCATCGTCATCTACACCGCCGGCCTGCCTCCGTCGCCGCCGAGTGGTGCCTCCGCCTACACGG
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 | 30.30% | 1.10% | 28.31% | 40.22% | NA |
| All Indica | 2759 | 2.40% | 0.00% | 36.46% | 61.07% | NA |
| All Japonica | 1512 | 83.70% | 3.40% | 9.46% | 3.44% | NA |
| Aus | 269 | 1.50% | 0.00% | 48.70% | 49.81% | NA |
| Indica I | 595 | 1.80% | 0.00% | 15.63% | 82.52% | NA |
| Indica II | 465 | 3.90% | 0.20% | 24.52% | 71.40% | NA |
| Indica III | 913 | 1.30% | 0.00% | 59.80% | 38.88% | NA |
| Indica Intermediate | 786 | 3.30% | 0.00% | 32.19% | 64.50% | NA |
| Temperate Japonica | 767 | 93.50% | 0.70% | 3.65% | 2.22% | NA |
| Tropical Japonica | 504 | 70.80% | 7.70% | 15.67% | 5.75% | NA |
| Japonica Intermediate | 241 | 79.70% | 2.90% | 14.94% | 2.49% | NA |
| VI/Aromatic | 96 | 55.20% | 1.00% | 38.54% | 5.21% | NA |
| Intermediate | 90 | 48.90% | 0.00% | 23.33% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0112723630 | G -> A | LOC_Os01g22620.1 | missense_variant ; p.Pro267Ser; MODERATE | nonsynonymous_codon ; P267S | Average:19.297; most accessible tissue: Minghui63 panicle, score: 50.413 | benign  |
0.388 |
TOLERATED | 0.13 |
| vg0112723630 | G -> DEL | LOC_Os01g22620.1 | N | frameshift_variant | Average:19.297; most accessible tissue: Minghui63 panicle, score: 50.413 | N | N | N | N |