Search for Variation information by Variation ID:
Detailed information for vg0401598934:
| Variant ID: vg0401598934 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 1598934 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 54. )
Flanking Sequence (100 bp) in Reference Genome:
ATGTAATTCATAGCCCTTTGGTACGTGGCTCCAGCACTTTTCAAGCCGAAAGTCATTACAACCCACTCAAACAAGCCGATCGCACCAGGACACCTGAAAG[C/T]
TGTCTTATGGATATCCTCTTCAGCCATGAAAATCTGATTATATCCTGCGTTCCCATCCATAAAACTCAATATTTTATGTCCTGAAGCTGCATCAACCAAC
Reverse complement sequence
GTTGGTTGATGCAGCTTCAGGACATAAAATATTGAGTTTTATGGATGGGAACGCAGGATATAATCAGATTTTCATGGCTGAAGAGGATATCCATAAGACA[G/A]
CTTTCAGGTGTCCTGGTGCGATCGGCTTGTTTGAGTGGGTTGTAATGACTTTCGGCTTGAAAAGTGCTGGAGCCACGTACCAAAGGGCTATGAATTACAT
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 | 76.90% | 16.60% | 1.93% | 4.55% | NA |
| All Indica | 2759 | 72.20% | 25.00% | 0.62% | 2.14% | NA |
| All Japonica | 1512 | 86.20% | 0.90% | 4.43% | 8.53% | NA |
| Aus | 269 | 60.60% | 28.30% | 1.49% | 9.67% | NA |
| Indica I | 595 | 64.90% | 32.40% | 1.18% | 1.51% | NA |
| Indica II | 465 | 81.90% | 17.40% | 0.43% | 0.22% | NA |
| Indica III | 913 | 70.50% | 25.60% | 0.44% | 3.40% | NA |
| Indica Intermediate | 786 | 74.00% | 23.20% | 0.51% | 2.29% | NA |
| Temperate Japonica | 767 | 78.10% | 0.30% | 6.26% | 15.38% | NA |
| Tropical Japonica | 504 | 97.20% | 1.40% | 0.99% | 0.40% | NA |
| Japonica Intermediate | 241 | 88.80% | 1.70% | 5.81% | 3.73% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 88.90% | 6.70% | 3.33% | 1.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0401598934 | C -> DEL | LOC_Os04g03630.1 | N | frameshift_variant | Average:32.009; most accessible tissue: Zhenshan97 flag leaf, score: 70.007 | N | N | N | N |
| vg0401598934 | C -> T | LOC_Os04g03630.1 | missense_variant ; p.Ala1314Thr; MODERATE | nonsynonymous_codon ; A1314T | Average:32.009; most accessible tissue: Zhenshan97 flag leaf, score: 70.007 | possibly damaging  |
1.646 |
TOLERATED | 0.06 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0401598934 | 3.56E-06 | 3.89E-07 | mr1565 | 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 |
| vg0401598934 | NA | 8.78E-06 | mr1332_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 |