Search for Variation information by Variation ID:
Detailed information for vg1124078708:
| Variant ID: vg1124078708 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 24078708 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.76, T: 0.23, others allele: 0.00, population size: 99. )
Flanking Sequence (100 bp) in Reference Genome:
ACATAGGCTTGTTGCGATGTGCCAGACCAGAATAACACGGGAGCATGTTGGTACCTCTGCAAGGCATGCCAACCAATAACGCTCTGCTCTGTCACTGACA[C/T]
GAGACAAAGGGAGGTCTCTTGACAAAAGATGACCCTCGAGATCCATGGAGCGGAGTGCTTGAATTACTGCTGCCTTCACATTCTTGGCCATACTGTCATT
Reverse complement sequence
AATGACAGTATGGCCAAGAATGTGAAGGCAGCAGTAATTCAAGCACTCCGCTCCATGGATCTCGAGGGTCATCTTTTGTCAAGAGACCTCCCTTTGTCTC[G/A]
TGTCAGTGACAGAGCAGAGCGTTATTGGTTGGCATGCCTTGCAGAGGTACCAACATGCTCCCGTGTTATTCTGGTCTGGCACATCGCAACAAGCCTATGT
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 | 37.40% | 18.60% | 1.27% | 42.74% | NA |
| All Indica | 2759 | 8.50% | 27.80% | 1.85% | 61.83% | NA |
| All Japonica | 1512 | 85.60% | 1.20% | 0.46% | 12.70% | NA |
| Aus | 269 | 50.90% | 17.50% | 0.00% | 31.60% | NA |
| Indica I | 595 | 5.20% | 3.00% | 1.51% | 90.25% | NA |
| Indica II | 465 | 6.50% | 23.40% | 2.58% | 67.53% | NA |
| Indica III | 913 | 10.30% | 45.60% | 1.31% | 42.83% | NA |
| Indica Intermediate | 786 | 10.20% | 28.50% | 2.29% | 59.03% | NA |
| Temperate Japonica | 767 | 92.00% | 0.70% | 0.13% | 7.17% | NA |
| Tropical Japonica | 504 | 85.70% | 1.20% | 0.60% | 12.50% | NA |
| Japonica Intermediate | 241 | 65.10% | 2.90% | 1.24% | 30.71% | NA |
| VI/Aromatic | 96 | 61.50% | 26.00% | 0.00% | 12.50% | NA |
| Intermediate | 90 | 45.60% | 24.40% | 2.22% | 27.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1124078708 | C -> T | LOC_Os11g40390.1 | missense_variant ; p.Arg163His; MODERATE | nonsynonymous_codon ; R163H | Average:14.358; most accessible tissue: Callus, score: 76.94 | benign  |
0.427 |
TOLERATED | 0.20 |
| vg1124078708 | C -> DEL | LOC_Os11g40390.1 | N | frameshift_variant | Average:14.358; most accessible tissue: Callus, score: 76.94 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1124078708 | 4.59E-06 | NA | mr1133 | 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 |
| vg1124078708 | 7.16E-07 | 2.68E-08 | mr1133 | Ind_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 |
| vg1124078708 | NA | 6.34E-06 | mr1395 | Ind_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 |
| vg1124078708 | NA | 7.86E-07 | mr1861 | Ind_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 |