Search for Variation information by Variation ID:
Detailed information for vg0612545907:
| Variant ID: vg0612545907 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 12545907 |
| 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: 103. )
Flanking Sequence (100 bp) in Reference Genome:
GCTTACAGTCTTAGGATCTAATTTCTTTAGTTGTGGATTAAATATTCTTGCCTCAGCACGACAGCCCCACACACGCAAATAATTTAATGTCGGTTTTCTT[C/T]
CGGTCCATAATTCATAAGGTGTTTTGGGTACCGACTTACTTGGAACTCGATTGAGTATGTGTGCAGCTGTTTTAAGTGCCTCTATCTATAAATTCACAGA
Reverse complement sequence
TCTGTGAATTTATAGATAGAGGCACTTAAAACAGCTGCACACATACTCAATCGAGTTCCAAGTAAGTCGGTACCCAAAACACCTTATGAATTATGGACCG[G/A]
AAGAAAACCGACATTAAATTATTTGCGTGTGTGGGGCTGTCGTGCTGAGGCAAGAATATTTAATCCACAACTAAAGAAATTAGATCCTAAGACTGTAAGC
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 | 85.80% | 7.20% | 6.81% | 0.23% | NA |
| All Indica | 2759 | 77.90% | 11.80% | 10.26% | 0.11% | NA |
| All Japonica | 1512 | 97.90% | 0.40% | 1.32% | 0.40% | NA |
| Aus | 269 | 94.10% | 1.50% | 4.46% | 0.00% | NA |
| Indica I | 595 | 91.90% | 2.40% | 5.71% | 0.00% | NA |
| Indica II | 465 | 83.20% | 9.90% | 6.88% | 0.00% | NA |
| Indica III | 913 | 70.50% | 15.90% | 13.36% | 0.22% | NA |
| Indica Intermediate | 786 | 72.50% | 15.30% | 12.09% | 0.13% | NA |
| Temperate Japonica | 767 | 98.30% | 0.00% | 0.91% | 0.78% | NA |
| Tropical Japonica | 504 | 97.60% | 0.40% | 1.98% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.10% | 1.70% | 1.24% | 0.00% | NA |
| VI/Aromatic | 96 | 93.80% | 0.00% | 4.17% | 2.08% | NA |
| Intermediate | 90 | 91.10% | 5.60% | 3.33% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0612545907 | C -> T | LOC_Os06g21700.1 | missense_variant ; p.Gly196Glu; MODERATE | nonsynonymous_codon ; G196K | Average:17.327; most accessible tissue: Minghui63 root, score: 29.362 | probably damaging  |
2.041 |
DELETERIOUS | 0.03 |
| vg0612545907 | C -> T | LOC_Os06g21700.1 | missense_variant ; p.Gly196Glu; MODERATE | nonsynonymous_codon ; G196E | Average:17.327; most accessible tissue: Minghui63 root, score: 29.362 | benign |
1.328 |
TOLERATED | 0.05 |
| vg0612545907 | C -> DEL | LOC_Os06g21700.1 | N | frameshift_variant | Average:17.327; most accessible tissue: Minghui63 root, score: 29.362 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0612545907 | 3.23E-06 | 3.66E-08 | mr1133_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 |