Search for Variation information by Variation ID:
Detailed information for vg1116233106:
| Variant ID: vg1116233106 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 16233106 |
| Reference Allele: GC | Alternative Allele: AC,G |
| Primary Allele: GC | Secondary Allele: AC |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GGGAGGTCCTGTCAAAAAGGTGGCCAAGAAGAAAGGACTCGTCGATGTCGCTCGCATTTTTAGCGACGACGAGTCCTCCGACGGGACTCCGACTTCGCCC[GC/AC,G]
TGATCACAGCCTGGATCTTTCGGCCGCCCCCATTCCTCCATTCGGCGCCGCTGGAGTAGACGGTAGCACCGCCGCGGGGGCTTCGGCTTCTGCGGAAAGG
Reverse complement sequence
CCTTTCCGCAGAAGCCGAAGCCCCCGCGGCGGTGCTACCGTCTACTCCAGCGGCGCCGAATGGAGGAATGGGGGCGGCCGAAAGATCCAGGCTGTGATCA[GC/GT,C]
GGGCGAAGTCGGAGTCCCGTCGGAGGACTCGTCGTCGCTAAAAATGCGAGCGACATCGACGAGTCCTTTCTTCTTGGCCACCTTTTTGACAGGACCTCCC
Allele Frequencies:
| Populations | Population Size | Frequency of GC(primary allele) | Frequency of AC(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 79.80% | 19.70% | 0.51% | 0.00% | G: 0.02% |
| All Indica | 2759 | 72.30% | 27.00% | 0.65% | 0.00% | G: 0.04% |
| All Japonica | 1512 | 98.70% | 1.30% | 0.00% | 0.00% | NA |
| Aus | 269 | 44.20% | 53.50% | 2.23% | 0.00% | NA |
| Indica I | 595 | 73.30% | 26.10% | 0.67% | 0.00% | NA |
| Indica II | 465 | 97.00% | 2.80% | 0.00% | 0.00% | G: 0.22% |
| Indica III | 913 | 57.90% | 41.30% | 0.77% | 0.00% | NA |
| Indica Intermediate | 786 | 73.50% | 25.60% | 0.89% | 0.00% | NA |
| Temperate Japonica | 767 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 98.40% | 1.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 81.10% | 18.90% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1116233106 | GC -> AC | LOC_Os11g28230.1 | missense_variant ; p.Ala615Thr; MODERATE | nonsynonymous_codon ; A615T | Average:33.251; most accessible tissue: Zhenshan97 flag leaf, score: 57.42 | benign  |
+0.383 |
N | N |
| vg1116233106 | GC -> G | LOC_Os11g28230.1 | frameshift_variant ; p.Ala615fs; HIGH | frameshift_variant | Average:33.251; most accessible tissue: Zhenshan97 flag leaf, score: 57.42 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1116233106 | NA | 7.57E-08 | mr1817 | Ind_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg1116233106 | NA | 3.25E-07 | mr1825 | Ind_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |