Search for Variation information by Variation ID:
Detailed information for vg0139514069:
| Variant ID: vg0139514069 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 39514069 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GTATGTCTCTTCAATGTATCGGATTATTGACCTTGGTTCATATGTGAGATTATCGATGACATGCGCATACATCTCAGATGCAACAAATGCACATGTAATG[C/T]
TCCTGTGGTATTTCTGAACACCAGGTAGAAAACATGTATGCTTGGTAACAACTGACACTGTCCAATAATTCTTCCATTTCCCCTTATACGCGTGCACTCT
Reverse complement sequence
AGAGTGCACGCGTATAAGGGGAAATGGAAGAATTATTGGACAGTGTCAGTTGTTACCAAGCATACATGTTTTCTACCTGGTGTTCAGAAATACCACAGGA[G/A]
CATTACATGTGCATTTGTTGCATCTGAGATGTATGCGCATGTCATCGATAATCTCACATATGAACCAAGGTCAATAATCCGATACATTGAAGAGACATAC
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 | 20.20% | 1.00% | 5.54% | 73.25% | NA |
| All Indica | 2759 | 1.40% | 0.00% | 2.28% | 96.27% | NA |
| All Japonica | 1512 | 58.40% | 3.00% | 10.65% | 27.91% | NA |
| Aus | 269 | 0.00% | 0.00% | 2.60% | 97.40% | NA |
| Indica I | 595 | 2.70% | 0.00% | 2.18% | 95.13% | NA |
| Indica II | 465 | 0.40% | 0.00% | 0.65% | 98.92% | NA |
| Indica III | 913 | 0.40% | 0.00% | 1.53% | 98.03% | NA |
| Indica Intermediate | 786 | 2.30% | 0.00% | 4.20% | 93.51% | NA |
| Temperate Japonica | 767 | 93.60% | 0.80% | 3.00% | 2.61% | NA |
| Tropical Japonica | 504 | 12.30% | 7.10% | 24.60% | 55.95% | NA |
| Japonica Intermediate | 241 | 42.70% | 1.70% | 5.81% | 49.79% | NA |
| VI/Aromatic | 96 | 2.10% | 0.00% | 22.92% | 75.00% | NA |
| Intermediate | 90 | 33.30% | 1.10% | 10.00% | 55.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0139514069 | C -> T | LOC_Os01g67990.1 | missense_variant ; p.Ser307Asn; MODERATE | nonsynonymous_codon ; S307N | Average:7.124; most accessible tissue: Callus, score: 29.745 | benign  |
-1.207 |
TOLERATED | 1.00 |
| vg0139514069 | C -> DEL | LOC_Os01g67990.1 | N | frameshift_variant | Average:7.124; most accessible tissue: Callus, score: 29.745 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0139514069 | NA | 8.94E-07 | mr1347_2 | Jap_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 |
| vg0139514069 | NA | 4.07E-07 | mr1696_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 |