Search for Variation information by Variation ID:
Detailed information for vg0224380989:
| Variant ID: vg0224380989 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 24380989 |
| Reference Allele: T | Alternative Allele: C,G |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 259. )
Flanking Sequence (100 bp) in Reference Genome:
CTTTATAGACATGGTTCACACATGATAGACCATGTCGACTTCATAGCCATCTGAATGCCGTCCAGATTACGGGCCAATATTTTTGAACTCTTTCCATATT[T/C,G]
TTGAGGTGTAAAAGACAAGCTTTCACATAGAAAATCGTCAAAATCATATTCTGTACCGAATCTACAGTTCCTGATAACACCATCGGGATGGCAACCCGAA
Reverse complement sequence
TTCGGGTTGCCATCCCGATGGTGTTATCAGGAACTGTAGATTCGGTACAGAATATGATTTTGACGATTTTCTATGTGAAAGCTTGTCTTTTACACCTCAA[A/G,C]
AATATGGAAAGAGTTCAAAAATATTGGCCCGTAATCTGGACGGCATTCAGATGGCTATGAAGTCGACATGGTCTATCATGTGTGAACCATGTCTATAAAG
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 | 72.30% | 5.10% | 1.86% | 20.78% | NA |
| All Indica | 2759 | 69.50% | 6.30% | 1.92% | 22.29% | NA |
| All Japonica | 1512 | 78.20% | 2.10% | 0.93% | 18.78% | NA |
| Aus | 269 | 74.70% | 4.50% | 1.86% | 18.96% | NA |
| Indica I | 595 | 67.40% | 11.80% | 1.01% | 19.83% | NA |
| Indica II | 465 | 70.30% | 3.40% | 2.80% | 23.44% | NA |
| Indica III | 913 | 66.20% | 5.40% | 1.97% | 26.51% | NA |
| Indica Intermediate | 786 | 74.60% | 4.80% | 2.04% | 18.58% | NA |
| Temperate Japonica | 767 | 89.00% | 2.20% | 0.65% | 8.08% | NA |
| Tropical Japonica | 504 | 62.10% | 1.00% | 1.39% | 35.52% | NA |
| Japonica Intermediate | 241 | 77.60% | 3.70% | 0.83% | 17.84% | NA |
| VI/Aromatic | 96 | 53.10% | 21.90% | 12.50% | 12.50% | NA |
| Intermediate | 90 | 71.10% | 2.20% | 4.44% | 22.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0224380989 | T -> G | LOC_Os02g40270.1 | missense_variant ; p.Lys384Gln; MODERATE | N | Average:67.852; most accessible tissue: Callus, score: 83.908 | N | N | N | N |
| vg0224380989 | T -> DEL | LOC_Os02g40270.1 | N | frameshift_variant | Average:67.852; most accessible tissue: Callus, score: 83.908 | N | N | N | N |
| vg0224380989 | T -> C | LOC_Os02g40270.1 | missense_variant ; p.Lys384Glu; MODERATE | nonsynonymous_codon ; K384E | Average:67.852; most accessible tissue: Callus, score: 83.908 | benign  |
0.883 |
DELETERIOUS | 0.03 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0224380989 | 2.37E-06 | 2.37E-06 | mr1384 | 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 |