Search for Variation information by Variation ID:
Detailed information for vg0115320554:
| Variant ID: vg0115320554 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 15320554 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TTCGAAGCCAGCTACCTCGGCCGAGATCACCAGGGGGTCTTGATGTGGGAACAACACTCCTTCGGCATCTTCTGGCCCAAAAGAGATCTGCTGGTTCAAA[T/C]
ATCGCGGGGCCCCTTCACTTGCCAAAGTGATGTTGTGCACCATTGGCAGCTGCATCTTCTTTTGCCCTTTTGACAGTTGATTCGGCGGGTCAGTCCTTGT
Reverse complement sequence
ACAAGGACTGACCCGCCGAATCAACTGTCAAAAGGGCAAAAGAAGATGCAGCTGCCAATGGTGCACAACATCACTTTGGCAAGTGAAGGGGCCCCGCGAT[A/G]
TTTGAACCAGCAGATCTCTTTTGGGCCAGAAGATGCCGAAGGAGTGTTGTTCCCACATCAAGACCCCCTGGTGATCTCGGCCGAGGTAGCTGGCTTCGAA
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 35.50% | 0.80% | 3.41% | 60.28% | NA |
| All Indica | 2759 | 8.20% | 1.20% | 4.82% | 85.76% | NA |
| All Japonica | 1512 | 85.40% | 0.00% | 0.07% | 14.48% | NA |
| Aus | 269 | 27.50% | 1.90% | 9.29% | 61.34% | NA |
| Indica I | 595 | 7.40% | 1.80% | 7.90% | 82.86% | NA |
| Indica II | 465 | 18.90% | 0.60% | 1.72% | 78.71% | NA |
| Indica III | 913 | 2.20% | 0.80% | 5.04% | 92.00% | NA |
| Indica Intermediate | 786 | 9.40% | 1.70% | 4.07% | 84.86% | NA |
| Temperate Japonica | 767 | 94.30% | 0.00% | 0.13% | 5.61% | NA |
| Tropical Japonica | 504 | 89.10% | 0.00% | 0.00% | 10.91% | NA |
| Japonica Intermediate | 241 | 49.80% | 0.00% | 0.00% | 50.21% | NA |
| VI/Aromatic | 96 | 37.50% | 0.00% | 2.08% | 60.42% | NA |
| Intermediate | 90 | 54.40% | 0.00% | 0.00% | 45.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0115320554 | T -> DEL | LOC_Os01g27440.1 | N | frameshift_variant | Average:13.975; most accessible tissue: Callus, score: 44.856 | N | N | N | N |
| vg0115320554 | T -> C | LOC_Os01g27440.1 | missense_variant ; p.Tyr391Cys; MODERATE | nonsynonymous_codon ; Y391C | Average:13.975; most accessible tissue: Callus, score: 44.856 | probably damaging  |
3.107 |
DELETERIOUS | 0.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0115320554 | 8.58E-06 | NA | mr1123 | 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 |
| vg0115320554 | 4.64E-07 | NA | mr1150 | 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 |
| vg0115320554 | 4.10E-06 | 7.80E-14 | mr1496 | 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 |