Search for Variation information by Variation ID:
Detailed information for vg0405892361:
| Variant ID: vg0405892361 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 5892361 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GTTGGAAGGTGTGGAATGTCACTGCCGGAAGATGGAGTGCGAAGACATCCCTTGCTCAGACATTTTTGTTGTACTCAAGTTCCTTGGTTTTGACACCATC[C/T]
CTCGTTGTTGTGTCGTGGATAGGTGGACAATGGGAGCAAAGGCGGCATTTAGGTCAGACAGGAATACCGATCCTAATGTGTGGTCTAAACACATGGTTCG
Reverse complement sequence
CGAACCATGTGTTTAGACCACACATTAGGATCGGTATTCCTGTCTGACCTAAATGCCGCCTTTGCTCCCATTGTCCACCTATCCACGACACAACAACGAG[G/A]
GATGGTGTCAAAACCAAGGAACTTGAGTACAACAAAAATGTCTGAGCAAGGGATGTCTTCGCACTCCATCTTCCGGCAGTGACATTCCACACCTTCCAAC
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 | 33.30% | 0.60% | 1.27% | 64.77% | NA |
| All Indica | 2759 | 16.90% | 1.00% | 1.78% | 80.32% | NA |
| All Japonica | 1512 | 64.70% | 0.10% | 0.33% | 34.92% | NA |
| Aus | 269 | 30.90% | 0.00% | 1.86% | 67.29% | NA |
| Indica I | 595 | 25.20% | 0.00% | 1.34% | 73.45% | NA |
| Indica II | 465 | 13.10% | 4.50% | 2.58% | 79.78% | NA |
| Indica III | 913 | 14.10% | 0.10% | 1.20% | 84.56% | NA |
| Indica Intermediate | 786 | 16.00% | 0.80% | 2.29% | 80.92% | NA |
| Temperate Japonica | 767 | 70.30% | 0.00% | 0.26% | 29.47% | NA |
| Tropical Japonica | 504 | 49.00% | 0.00% | 0.40% | 50.60% | NA |
| Japonica Intermediate | 241 | 79.70% | 0.40% | 0.41% | 19.50% | NA |
| VI/Aromatic | 96 | 17.70% | 0.00% | 0.00% | 82.29% | NA |
| Intermediate | 90 | 34.40% | 1.10% | 1.11% | 63.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0405892361 | C -> DEL | LOC_Os04g10860.1 | N | frameshift_variant | Average:7.921; most accessible tissue: Callus, score: 17.56 | N | N | N | N |
| vg0405892361 | C -> T | LOC_Os04g10860.1 | missense_variant ; p.Pro413Ser; MODERATE | nonsynonymous_codon ; P413S | Average:7.921; most accessible tissue: Callus, score: 17.56 | possibly damaging  |
1.984 |
DELETERIOUS | 0.03 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0405892361 | 3.81E-06 | 2.34E-06 | mr1879_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 |