Search for Variation information by Variation ID:
Detailed information for vg0714855686:
| Variant ID: vg0714855686 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 14855686 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.03, others allele: 0.00, population size: 154. )
Flanking Sequence (100 bp) in Reference Genome:
ACAGACAGTTGGAACCAACCGTCAAAACCTTCCGGATTTCCACAAACTCTACTACTGAAGGTTTAGGGATTATCTCTGGAGTGCCCACACGGCACAACAA[C/T]
GTTGAGGTCATCTTAGATTTCCATGTGTTCGACATCTCTGATTTCGACATACTCATAGGCCATCCCATAGAGAAACTCTTAGATGTGCCCGAAACCGGTA
Reverse complement sequence
TACCGGTTTCGGGCACATCTAAGAGTTTCTCTATGGGATGGCCTATGAGTATGTCGAAATCAGAGATGTCGAACACATGGAAATCTAAGATGACCTCAAC[G/A]
TTGTTGTGCCGTGTGGGCACTCCAGAGATAATCCCTAAACCTTCAGTAGTAGAGTTTGTGGAAATCCGGAAGGTTTTGACGGTTGGTTCCAACTGTCTGT
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 | 88.70% | 4.90% | 3.15% | 3.26% | NA |
| All Indica | 2759 | 82.90% | 8.40% | 4.02% | 4.64% | NA |
| All Japonica | 1512 | 99.10% | 0.00% | 0.46% | 0.40% | NA |
| Aus | 269 | 84.40% | 0.00% | 10.41% | 5.20% | NA |
| Indica I | 595 | 90.60% | 1.20% | 5.21% | 3.03% | NA |
| Indica II | 465 | 66.50% | 23.40% | 4.95% | 5.16% | NA |
| Indica III | 913 | 85.70% | 5.40% | 2.74% | 6.24% | NA |
| Indica Intermediate | 786 | 83.70% | 8.50% | 4.07% | 3.69% | NA |
| Temperate Japonica | 767 | 99.20% | 0.00% | 0.26% | 0.52% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.00% | 2.07% | 0.83% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 90.00% | 0.00% | 3.33% | 6.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0714855686 | C -> DEL | LOC_Os07g25860.1 | N | frameshift_variant | Average:12.963; most accessible tissue: Callus, score: 41.561 | N | N | N | N |
| vg0714855686 | C -> T | LOC_Os07g25860.1 | synonymous_variant ; p.Asn285Asn; LOW | synonymous_codon | Average:12.963; most accessible tissue: Callus, score: 41.561 | N | N | N | N |
| vg0714855686 | C -> T | LOC_Os07g25860.1 | synonymous_variant ; p.Asn285Asn; LOW | nonsynonymous_codon | Average:12.963; most accessible tissue: Callus, score: 41.561 | benign  |
-0.276 |
TOLERATED | 0.29 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0714855686 | 2.19E-06 | 2.19E-06 | mr1584_2 | Ind_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 |