Search for Variation information by Variation ID:
Detailed information for vg1105974351:
| Variant ID: vg1105974351 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5974351 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, T: 0.05, others allele: 0.00, population size: 76. )
Flanking Sequence (100 bp) in Reference Genome:
TGATAGCCACCCATTTTATTATTGCCGAAATCTTTTTTCGACAGCGTGGTGTCGGACCTGAGCCTGCACATGGTGCTGGAGGCCGGCGAGCACCGCGGCA[G/T]
CTCGGTGACGGCGAAGGGCCGCATCGACATGGACGCCGGGGAGCGCGAGTCGGTGGTGATCGGCGGCACGGGGCGGTTTCGGCTCGCGCGCGGGTACATG
Reverse complement sequence
CATGTACCCGCGCGCGAGCCGAAACCGCCCCGTGCCGCCGATCACCACCGACTCGCGCTCCCCGGCGTCCATGTCGATGCGGCCCTTCGCCGTCACCGAG[C/A]
TGCCGCGGTGCTCGCCGGCCTCCAGCACCATGTGCAGGCTCAGGTCCGACACCACGCTGTCGAAAAAAGATTTCGGCAATAATAAAATGGGTGGCTATCA
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 | 95.20% | 4.30% | 0.15% | 0.34% | NA |
| All Indica | 2759 | 96.00% | 3.60% | 0.18% | 0.25% | NA |
| All Japonica | 1512 | 92.70% | 6.60% | 0.07% | 0.60% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.37% | 0.00% | NA |
| Indica I | 595 | 99.00% | 0.20% | 0.34% | 0.50% | NA |
| Indica II | 465 | 97.40% | 2.20% | 0.00% | 0.43% | NA |
| Indica III | 913 | 93.90% | 5.80% | 0.22% | 0.11% | NA |
| Indica Intermediate | 786 | 95.30% | 4.50% | 0.13% | 0.13% | NA |
| Temperate Japonica | 767 | 96.60% | 2.10% | 0.13% | 1.17% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1105974351 | G -> T | LOC_Os11g10840.1 | missense_variant ; p.Ser11Ile; MODERATE | nonsynonymous_codon ; S11I | Average:20.775; most accessible tissue: Callus, score: 34.526 | possibly damaging  |
1.948 |
DELETERIOUS | 0.02 |
| vg1105974351 | G -> DEL | LOC_Os11g10840.1 | N | frameshift_variant | Average:20.775; 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 |
|---|---|---|---|---|---|---|
| vg1105974351 | 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 |
| vg1105974351 | 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 |
| vg1105974351 | 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 |