Search for Variation information by Variation ID:
Detailed information for vg0802885223:
| Variant ID: vg0802885223 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 2885223 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GGGTGCTTATACAGTTCTTCTACTATTCTAGGTTTTTTATCGTTATAGATGACATATGGGATAAGCCATCATGGCAAATACTCGAAAGTGGTTTACAAGA[T/C]
AATGATTACGGAAGTAAAATACTTGTAACTACTCGTAAATCTGAGGTTGCAACAATTATCAGCGATGTGTACAATATGAAACCACTTTCTCATGATAACT
Reverse complement sequence
AGTTATCATGAGAAAGTGGTTTCATATTGTACACATCGCTGATAATTGTTGCAACCTCAGATTTACGAGTAGTTACAAGTATTTTACTTCCGTAATCATT[A/G]
TCTTGTAAACCACTTTCGAGTATTTGCCATGATGGCTTATCCCATATGTCATCTATAACGATAAAAAACCTAGAATAGTAGAAGAACTGTATAAGCACCC
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 | 44.00% | 19.70% | 4.76% | 31.53% | NA |
| All Indica | 2759 | 20.10% | 32.90% | 5.55% | 41.43% | NA |
| All Japonica | 1512 | 79.60% | 0.50% | 3.97% | 16.01% | NA |
| Aus | 269 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 8.40% | 45.20% | 10.59% | 35.80% | NA |
| Indica II | 465 | 14.60% | 23.70% | 5.81% | 55.91% | NA |
| Indica III | 913 | 25.50% | 33.80% | 0.77% | 39.87% | NA |
| Indica Intermediate | 786 | 25.80% | 28.10% | 7.12% | 38.93% | NA |
| Temperate Japonica | 767 | 88.50% | 0.30% | 3.65% | 7.56% | NA |
| Tropical Japonica | 504 | 81.00% | 0.60% | 1.59% | 16.87% | NA |
| Japonica Intermediate | 241 | 48.10% | 0.80% | 9.96% | 41.08% | NA |
| VI/Aromatic | 96 | 11.50% | 2.10% | 8.33% | 78.12% | NA |
| Intermediate | 90 | 51.10% | 11.10% | 4.44% | 33.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0802885223 | T -> C | LOC_Os08g05440.1 | synonymous_variant ; p.Asp577Asp; LOW | synonymous_codon | Average:56.03; most accessible tissue: Callus, score: 83.97 | N | N | N | N |
| vg0802885223 | T -> C | LOC_Os08g05440.1 | synonymous_variant ; p.Asp577Asp; LOW | nonsynonymous_codon ; D577H | Average:56.03; most accessible tissue: Callus, score: 83.97 | probably damaging  |
2.561 |
TOLERATED | 0.07 |
| vg0802885223 | T -> DEL | LOC_Os08g05440.1 | N | frameshift_variant | Average:56.03; most accessible tissue: Callus, score: 83.97 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0802885223 | NA | 8.78E-07 | mr1227_2 | 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 |
| vg0802885223 | NA | 1.53E-07 | mr1272_2 | 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 |
| vg0802885223 | NA | 4.03E-06 | mr1790_2 | 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 |
| vg0802885223 | NA | 8.22E-12 | mr1940_2 | 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 |