Search for Variation information by Variation ID:
Detailed information for vg1105974344:
| Variant ID: vg1105974344 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5974344 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.05, others allele: 0.00, population size: 77. )
Flanking Sequence (100 bp) in Reference Genome:
TCTAGCTTGATAGCCACCCATTTTATTATTGCCGAAATCTTTTTTCGACAGCGTGGTGTCGGACCTGAGCCTGCACATGGTGCTGGAGGCCGGCGAGCAC[C/T]
GCGGCAGCTCGGTGACGGCGAAGGGCCGCATCGACATGGACGCCGGGGAGCGCGAGTCGGTGGTGATCGGCGGCACGGGGCGGTTTCGGCTCGCGCGCGG
Reverse complement sequence
CCGCGCGCGAGCCGAAACCGCCCCGTGCCGCCGATCACCACCGACTCGCGCTCCCCGGCGTCCATGTCGATGCGGCCCTTCGCCGTCACCGAGCTGCCGC[G/A]
GTGCTCGCCGGCCTCCAGCACCATGTGCAGGCTCAGGTCCGACACCACGCTGTCGAAAAAAGATTTCGGCAATAATAAAATGGGTGGCTATCAAGCTAGA
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 | 95.10% | 4.30% | 0.28% | 0.36% | NA |
| All Indica | 2759 | 95.80% | 3.60% | 0.40% | 0.25% | NA |
| All Japonica | 1512 | 92.60% | 6.60% | 0.13% | 0.66% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.30% | 0.20% | 1.01% | 0.50% | NA |
| Indica II | 465 | 97.00% | 2.20% | 0.22% | 0.65% | NA |
| Indica III | 913 | 94.00% | 5.80% | 0.11% | 0.11% | NA |
| Indica Intermediate | 786 | 95.30% | 4.30% | 0.38% | 0.00% | NA |
| Temperate Japonica | 767 | 96.30% | 2.10% | 0.26% | 1.30% | NA |
| Tropical Japonica | 504 | 86.70% | 13.30% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 92.90% | 7.10% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 4.40% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1105974344 | C -> T | LOC_Os11g10840.1 | missense_variant ; p.Arg9Cys; MODERATE | nonsynonymous_codon ; R9C | Average:20.68; most accessible tissue: Callus, score: 34.526 | probably damaging  |
3.207 |
DELETERIOUS | 0.03 |
| vg1105974344 | C -> DEL | LOC_Os11g10840.1 | N | frameshift_variant | Average:20.68; most accessible tissue: Callus, score: 34.526 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1105974344 | NA | 4.10E-06 | mr1236 | Jap_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 |
| vg1105974344 | NA | 1.57E-10 | mr1248 | Jap_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 |
| vg1105974344 | NA | 4.59E-06 | mr1522_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 |