Search for Variation information by Variation ID:
Detailed information for vg1113568071:
| Variant ID: vg1113568071 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 13568071 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CTCGTCAGTCTGTTACCCGGCAGAGATAGCGGAGGATGTGCCAGTCAAGATACGGGATTTCTTCATCCCGGTTGACTTTGTGGTGCTGGACATGGACATA[G/A]
GAAAAGAGACGCCGCTCATCCTGGGTGTCACGCCCTGAAAATCGCCTAAATTAATAATCCATATTTTAAATCATTTTTAGAAATTATTTTAAAAGCCTTC
Reverse complement sequence
GAAGGCTTTTAAAATAATTTCTAAAAATGATTTAAAATATGGATTATTAATTTAGGCGATTTTCAGGGCGTGACACCCAGGATGAGCGGCGTCTCTTTTC[C/T]
TATGTCCATGTCCAGCACCACAAAGTCAACCGGGATGAAGAAATCCCGTATCTTGACTGGCACATCCTCCGCTATCTCTGCCGGGTAACAGACTGACGAG
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 | 96.80% | 0.50% | 0.30% | 2.35% | NA |
| All Indica | 2759 | 95.80% | 0.60% | 0.47% | 3.12% | NA |
| All Japonica | 1512 | 98.60% | 0.30% | 0.07% | 1.06% | NA |
| Aus | 269 | 99.30% | 0.00% | 0.00% | 0.74% | NA |
| Indica I | 595 | 95.50% | 0.20% | 1.01% | 3.36% | NA |
| Indica II | 465 | 96.10% | 0.00% | 0.22% | 3.66% | NA |
| Indica III | 913 | 99.90% | 0.00% | 0.00% | 0.11% | NA |
| Indica Intermediate | 786 | 91.10% | 2.00% | 0.76% | 6.11% | NA |
| Temperate Japonica | 767 | 97.80% | 0.40% | 0.13% | 1.69% | NA |
| Tropical Japonica | 504 | 99.20% | 0.20% | 0.00% | 0.60% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 94.80% | 3.10% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 94.40% | 0.00% | 0.00% | 5.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1113568071 | G -> A | LOC_Os11g23950.1 | missense_variant ; p.Gly59Arg; MODERATE | nonsynonymous_codon ; G59R | Average:31.341; most accessible tissue: Zhenshan97 flag leaf, score: 46.427 | benign  |
1.001 |
TOLERATED | 0.14 |
| vg1113568071 | G -> DEL | LOC_Os11g23950.1 | N | frameshift_variant | Average:31.341; most accessible tissue: Zhenshan97 flag leaf, score: 46.427 | N | N | N | N |