Search for Variation information by Variation ID:
Detailed information for vg0610861016:
| Variant ID: vg0610861016 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr06 | Position: 10861016 |
| Reference Allele: C | Alternative Allele: T,CGT |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CCACCCCTTGACGAACATGTGCCACCTCCTAAGCCAGATACATCCAAGGAGCAGCCAACTACCTGTGAAGCCTGCAAGCTCATACCTGTTATGGTTTCCA[C/T,CGT]
GTACAACAAGGAGAAAATGGTAGAGTATGAGATGCGGATGGTTTTGCAGTCTTTCAACGGTCGAGGGGGTCCGCTAAAGCCAGTTGGACCTGATCAGTAT
Reverse complement sequence
ATACTGATCAGGTCCAACTGGCTTTAGCGGACCCCCTCGACCGTTGAAAGACTGCAAAACCATCCGCATCTCATACTCTACCATTTTCTCCTTGTTGTAC[G/A,ACG]
TGGAAACCATAACAGGTATGAGCTTGCAGGCTTCACAGGTAGTTGGCTGCTCCTTGGATGTATCTGGCTTAGGAGGTGGCACATGTTCGTCAAGGGGTGG
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 86.00% | 2.60% | 3.26% | 7.89% | CGT: 0.34% |
| All Indica | 2759 | 77.10% | 4.20% | 5.44% | 12.83% | CGT: 0.43% |
| All Japonica | 1512 | 99.20% | 0.10% | 0.00% | 0.66% | NA |
| Aus | 269 | 97.00% | 0.00% | 1.12% | 0.37% | CGT: 1.49% |
| Indica I | 595 | 54.10% | 5.00% | 8.24% | 32.27% | CGT: 0.34% |
| Indica II | 465 | 66.20% | 10.10% | 10.54% | 12.69% | CGT: 0.43% |
| Indica III | 913 | 95.70% | 1.10% | 1.53% | 1.53% | CGT: 0.11% |
| Indica Intermediate | 786 | 79.30% | 3.70% | 4.83% | 11.32% | CGT: 0.89% |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.00% | 0.26% | NA |
| Tropical Japonica | 504 | 98.40% | 0.40% | 0.00% | 1.19% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 86.70% | 3.30% | 1.11% | 8.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0610861016 | C -> T | LOC_Os06g19090.1 | missense_variant ; p.Thr225Met; MODERATE | nonsynonymous_codon ; T225M | Average:27.526; most accessible tissue: Callus, score: 57.105 | benign  |
0.525 |
DELETERIOUS | 0.02 |
| vg0610861016 | C -> DEL | LOC_Os06g19090.1 | N | frameshift_variant | Average:27.526; most accessible tissue: Callus, score: 57.105 | N | N | N | N |
| vg0610861016 | C -> CGT | LOC_Os06g19090.1 | frameshift_variant ; p.Tyr226fs; HIGH | frameshift_variant | Average:27.526; most accessible tissue: Callus, score: 57.105 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0610861016 | 5.53E-06 | 6.94E-08 | mr1850 | 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 |