Search for Variation information by Variation ID:
Detailed information for vg0801634692:
| Variant ID: vg0801634692 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr08 | Position: 1634692 |
| Reference Allele: G | Alternative Allele: T,GTCAA |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CGTCGGGTACAGCCTCAAGAGGTGCCTCGCCGCCGGCGAGTTCGTCCGGTCCTCCGCCTTCGCCGCCTGCGGCTACAGGTGGTCCGTCCGCGTCTACCCC[G/T,GTCAA]
GCGGGTTCGGGCCGGCGCACCGGGAGTTCGTGTCGGTGTTCGTCAAGATGATGACCAACAGGGGCAAGGCGGCGGCGCGGTTCGACCTCCGGCTGATCGA
Reverse complement sequence
TCGATCAGCCGGAGGTCGAACCGCGCCGCCGCCTTGCCCCTGTTGGTCATCATCTTGACGAACACCGACACGAACTCCCGGTGCGCCGGCCCGAACCCGC[C/A,TTGAC]
GGGGTAGACGCGGACGGACCACCTGTAGCCGCAGGCGGCGAAGGCGGAGGACCGGACGAACTCGCCGGCGGCGAGGCACCTCTTGAGGCTGTACCCGACG
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 93.90% | 5.30% | 0.06% | 0.72% | GTCAA: 0.02% |
| All Indica | 2759 | 97.60% | 1.10% | 0.04% | 1.23% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 19.70% | 80.30% | 0.00% | 0.00% | NA |
| Indica I | 595 | 97.60% | 0.00% | 0.00% | 2.35% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.50% | 0.80% | 0.00% | 0.77% | NA |
| Indica Intermediate | 786 | 95.40% | 2.80% | 0.13% | 1.65% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 96.90% | 2.10% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 3.30% | 1.11% | 0.00% | GTCAA: 1.11% |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0801634692 | G -> T | LOC_Os08g03490.1 | missense_variant ; p.Gly64Cys; MODERATE | nonsynonymous_codon ; G64C | Average:78.459; most accessible tissue: Minghui63 flag leaf, score: 83.197 | probably damaging  |
3.263 |
DELETERIOUS | 0.00 |
| vg0801634692 | G -> GTCAA | LOC_Os08g03490.1 | frameshift_variant ; p.Gly64fs; HIGH | frameshift_variant | Average:78.459; most accessible tissue: Minghui63 flag leaf, score: 83.197 | N | N | N | N |
| vg0801634692 | G -> DEL | LOC_Os08g03490.1 | N | frameshift_variant | Average:78.459; most accessible tissue: Minghui63 flag leaf, score: 83.197 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0801634692 | NA | 1.93E-06 | mr1344_2 | 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 |
| vg0801634692 | NA | 1.05E-07 | mr1510_2 | 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 |
| vg0801634692 | NA | 1.32E-15 | mr1587_2 | 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 |
| vg0801634692 | NA | 1.84E-12 | mr1803_2 | 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 |