Search for Variation information by Variation ID:
Detailed information for vg0112723202:
| Variant ID: vg0112723202 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 12723202 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ACCAGTCGGCGGCGACGAAGGCGGTCGACGGTGAAAGCGAAGATGCCCACTAATGGCGGCATAATAGGTCAGCCGTGTAAGCGGAAACACCAGTCGACGG[C/G]
AACGAAGGTGAGCCAACGGTGACGATGTAGACATCCAACAACGGCGGCATAATAGGCCAGCCGTGTAGGAGGAGGCACCACTCGGCGGCGACGGAGGCAG
Reverse complement sequence
CTGCCTCCGTCGCCGCCGAGTGGTGCCTCCTCCTACACGGCTGGCCTATTATGCCGCCGTTGTTGGATGTCTACATCGTCACCGTTGGCTCACCTTCGTT[G/C]
CCGTCGACTGGTGTTTCCGCTTACACGGCTGACCTATTATGCCGCCATTAGTGGGCATCTTCGCTTTCACCGTCGACCGCCTTCGTCGCCGCCGACTGGT
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 54.90% | 0.20% | 14.30% | 30.62% | NA |
| All Indica | 2759 | 32.70% | 0.00% | 19.46% | 47.81% | NA |
| All Japonica | 1512 | 90.30% | 0.50% | 7.54% | 1.65% | NA |
| Aus | 269 | 63.90% | 0.00% | 5.20% | 30.86% | NA |
| Indica I | 595 | 16.60% | 0.00% | 5.21% | 78.15% | NA |
| Indica II | 465 | 22.60% | 0.00% | 36.56% | 40.86% | NA |
| Indica III | 913 | 49.00% | 0.00% | 21.80% | 29.24% | NA |
| Indica Intermediate | 786 | 32.10% | 0.00% | 17.43% | 50.51% | NA |
| Temperate Japonica | 767 | 96.00% | 0.00% | 3.26% | 0.78% | NA |
| Tropical Japonica | 504 | 83.90% | 1.00% | 12.10% | 2.98% | NA |
| Japonica Intermediate | 241 | 85.90% | 0.80% | 11.62% | 1.66% | NA |
| VI/Aromatic | 96 | 94.80% | 0.00% | 2.08% | 3.12% | NA |
| Intermediate | 90 | 67.80% | 3.30% | 10.00% | 18.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0112723202 | C -> G | LOC_Os01g22620.1 | missense_variant ; p.Leu409Phe; MODERATE | nonsynonymous_codon ; L409F | Average:16.907; most accessible tissue: Zhenshan97 flag leaf, score: 29.417 | possibly damaging  |
1.609 |
TOLERATED | 0.19 |
| vg0112723202 | C -> DEL | LOC_Os01g22620.1 | N | frameshift_variant | Average:16.907; most accessible tissue: Zhenshan97 flag leaf, score: 29.417 | N | N | N | N |