Search for Variation information by Variation ID:
Detailed information for vg1206877221:
| Variant ID: vg1206877221 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 6877221 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.94, C: 0.05, others allele: 0.00, population size: 200. )
Flanking Sequence (100 bp) in Reference Genome:
CTCCCCCTGAACTGTGACAAAGTACCTCCAATATCGGGTCTAGTTCCTGGACTAGCCTCATCAAAAGAAACTTCGCAAGTCTCAACAATTTTATTAGTTT[T/C]
CAAAACAAGTACACGATAGCCACGTGAATGTGCGGGGTAACCAAGAAACATTCCATCGGTAGAACGTGCTTCAAACTTGTCTAAATTTCCAGATTTCAAG
Reverse complement sequence
CTTGAAATCTGGAAATTTAGACAAGTTTGAAGCACGTTCTACCGATGGAATGTTTCTTGGTTACCCCGCACATTCACGTGGCTATCGTGTACTTGTTTTG[A/G]
AAACTAATAAAATTGTTGAGACTTGCGAAGTTTCTTTTGATGAGGCTAGTCCAGGAACTAGACCCGATATTGGAGGTACTTTGTCACAGTTCAGGGGGAG
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 58.50% | 1.80% | 11.28% | 28.42% | NA |
| All Indica | 2759 | 32.90% | 0.60% | 18.81% | 47.70% | NA |
| All Japonica | 1512 | 96.40% | 2.60% | 0.33% | 0.73% | NA |
| Aus | 269 | 94.40% | 1.90% | 2.23% | 1.49% | NA |
| Indica I | 595 | 38.30% | 0.00% | 12.27% | 49.41% | NA |
| Indica II | 465 | 25.60% | 0.20% | 10.97% | 63.23% | NA |
| Indica III | 913 | 26.90% | 0.90% | 30.12% | 42.06% | NA |
| Indica Intermediate | 786 | 39.90% | 1.00% | 15.27% | 43.77% | NA |
| Temperate Japonica | 767 | 94.50% | 5.00% | 0.00% | 0.52% | NA |
| Tropical Japonica | 504 | 98.00% | 0.00% | 0.79% | 1.19% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.40% | 0.41% | 0.41% | NA |
| VI/Aromatic | 96 | 83.30% | 15.60% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 76.70% | 7.80% | 2.22% | 13.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1206877221 | T -> C | LOC_Os12g12480.1 | missense_variant ; p.Lys216Glu; MODERATE | nonsynonymous_codon ; K216E | Average:43.491; most accessible tissue: Zhenshan97 flag leaf, score: 57.42 | benign  |
-1.357 |
TOLERATED | 1.00 |
| vg1206877221 | T -> DEL | LOC_Os12g12480.1 | N | frameshift_variant | Average:43.491; most accessible tissue: Zhenshan97 flag leaf, score: 57.42 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1206877221 | 7.03E-07 | 2.72E-07 | mr1940 | Jap_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 |