Search for Variation information by Variation ID:
Detailed information for vg0707251524:
| Variant ID: vg0707251524 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 7251524 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TTTCTATACATCTTCTCACACTTCTTATTTTTTGCACTCAAAATATTAATAGCTTCCTCAAAAGCACTCACCTCATTATCTTCATACTCTATATCAGATT[T/C]
ACCACGCGCCATGAAGCAAACATCGGAGACGTTATTTCCCTTATCATCATCTCCACTTTCACCATCTATATCACTTAGTGGCTCGAAGACGGCGCAAACT
Reverse complement sequence
AGTTTGCGCCGTCTTCGAGCCACTAAGTGATATAGATGGTGAAAGTGGAGATGATGATAAGGGAAATAACGTCTCCGATGTTTGCTTCATGGCGCGTGGT[A/G]
AATCTGATATAGAGTATGAAGATAATGAGGTGAGTGCTTTTGAGGAAGCTATTAATATTTTGAGTGCAAAAAATAAGAAGTGTGAGAAGATGTATAGAAA
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 | 35.90% | 5.40% | 2.71% | 56.05% | NA |
| All Indica | 2759 | 7.50% | 0.40% | 4.02% | 88.04% | NA |
| All Japonica | 1512 | 79.60% | 15.70% | 0.00% | 4.76% | NA |
| Aus | 269 | 62.50% | 0.00% | 5.20% | 32.34% | NA |
| Indica I | 595 | 6.40% | 0.00% | 3.03% | 90.59% | NA |
| Indica II | 465 | 8.60% | 1.50% | 3.44% | 86.45% | NA |
| Indica III | 913 | 1.40% | 0.30% | 3.83% | 94.41% | NA |
| Indica Intermediate | 786 | 14.90% | 0.10% | 5.34% | 79.64% | NA |
| Temperate Japonica | 767 | 96.20% | 2.90% | 0.00% | 0.91% | NA |
| Tropical Japonica | 504 | 67.30% | 21.00% | 0.00% | 11.71% | NA |
| Japonica Intermediate | 241 | 52.30% | 45.20% | 0.00% | 2.49% | NA |
| VI/Aromatic | 96 | 77.10% | 0.00% | 0.00% | 22.92% | NA |
| Intermediate | 90 | 47.80% | 5.60% | 3.33% | 43.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0707251524 | T -> DEL | LOC_Os07g12690.1 | N | frameshift_variant | Average:6.76; most accessible tissue: Callus, score: 21.413 | N | N | N | N |
| vg0707251524 | T -> C | LOC_Os07g12690.1 | missense_variant ; p.Lys369Glu; MODERATE | nonsynonymous_codon ; K369E | Average:6.76; most accessible tissue: Callus, score: 21.413 | benign  |
-1.285 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0707251524 | 2.34E-06 | 2.34E-06 | mr1177_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 |