Search for Variation information by Variation ID:
Detailed information for vg0727210166:
| Variant ID: vg0727210166 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 27210166 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 126. )
Flanking Sequence (100 bp) in Reference Genome:
TACACTCTTAGCAAGGCAGAGAAGGAAAGTATGTTTGAATGCTTGGAGAGCATCAAGGTACCGTCTGGATACTCCACGAACATAAAGCGAATAATAAGCA[C/T]
GAAGGAGAAGAAGTTCACAAACCTAAAGTCTCATGACTATCACGTGTTGATGACACAATTGCTACCAGTTATAATTCGGGGTATCCTTCCAGACAATGTC
Reverse complement sequence
GACATTGTCTGGAAGGATACCCCGAATTATAACTGGTAGCAATTGTGTCATCAACACGTGATAGTCATGAGACTTTAGGTTTGTGAACTTCTTCTCCTTC[G/A]
TGCTTATTATTCGCTTTATGTTCGTGGAGTATCCAGACGGTACCTTGATGCTCTCCAAGCATTCAAACATACTTTCCTTCTCTGCCTTGCTAAGAGTGTA
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 | 89.40% | 7.70% | 2.54% | 0.36% | NA |
| All Indica | 2759 | 85.80% | 10.50% | 3.26% | 0.47% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 63.60% | 24.50% | 10.41% | 1.49% | NA |
| Indica I | 595 | 98.00% | 1.20% | 0.84% | 0.00% | NA |
| Indica II | 465 | 66.20% | 29.20% | 4.30% | 0.22% | NA |
| Indica III | 913 | 87.60% | 7.80% | 3.61% | 0.99% | NA |
| Indica Intermediate | 786 | 86.00% | 9.50% | 4.07% | 0.38% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 94.80% | 3.10% | 2.08% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 7.80% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0727210166 | C -> DEL | LOC_Os07g45590.1 | N | frameshift_variant | Average:17.699; most accessible tissue: Minghui63 young leaf, score: 24.836 | N | N | N | N |
| vg0727210166 | C -> T | LOC_Os07g45590.1 | missense_variant ; p.Thr198Met; MODERATE | nonsynonymous_codon ; T198M | Average:17.699; most accessible tissue: Minghui63 young leaf, score: 24.836 | benign  |
1.119 |
DELETERIOUS | 0.03 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0727210166 | NA | 4.19E-06 | mr1072 | 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 |
| vg0727210166 | NA | 2.77E-06 | mr1441 | 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 |
| vg0727210166 | 1.58E-06 | 1.59E-06 | mr1562 | 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 |
| vg0727210166 | 8.35E-06 | 8.35E-06 | mr1562 | 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 |
| vg0727210166 | NA | 8.28E-06 | mr1609 | 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 |