Search for Variation information by Variation ID:
Detailed information for vg1113568070:
| Variant ID: vg1113568070 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 13568070 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 107. )
Flanking Sequence (100 bp) in Reference Genome:
ACTCGTCAGTCTGTTACCCGGCAGAGATAGCGGAGGATGTGCCAGTCAAGATACGGGATTTCTTCATCCCGGTTGACTTTGTGGTGCTGGACATGGACAT[A/G]
GGAAAAGAGACGCCGCTCATCCTGGGTGTCACGCCCTGAAAATCGCCTAAATTAATAATCCATATTTTAAATCATTTTTAGAAATTATTTTAAAAGCCTT
Reverse complement sequence
AAGGCTTTTAAAATAATTTCTAAAAATGATTTAAAATATGGATTATTAATTTAGGCGATTTTCAGGGCGTGACACCCAGGATGAGCGGCGTCTCTTTTCC[T/C]
ATGTCCATGTCCAGCACCACAAAGTCAACCGGGATGAAGAAATCCCGTATCTTGACTGGCACATCCTCCGCTATCTCTGCCGGGTAACAGACTGACGAGT
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 | 63.60% | 36.40% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 94.70% | 5.30% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 4.20% | 95.80% | 0.00% | 0.00% | NA |
| Aus | 269 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 92.60% | 7.40% | 0.00% | 0.00% | NA |
| Indica II | 465 | 95.70% | 4.30% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 90.20% | 9.80% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 2.10% | 97.90% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 8.10% | 91.90% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 2.50% | 97.50% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 12.50% | 87.50% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 57.80% | 41.10% | 1.11% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1113568070 | A -> G | LOC_Os11g23950.1 | missense_variant ; p.Ile58Met; MODERATE | nonsynonymous_codon ; I58M | Average:31.341; most accessible tissue: Zhenshan97 flag leaf, score: 46.427 | benign  |
-0.045 |
TOLERATED | 0.09 |