Search for Variation information by Variation ID:
Detailed information for vg0714435734:
| Variant ID: vg0714435734 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 14435734 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AGTTGTAACTGTTCATGCATTGCCCTCTGAACCTCGAAGGTCAAGTCTAAACCAAATAACTTTGGAAGAGATTCCTATAGTCCGGGAGTACCCTGATGTG[T/C]
TCCCTGATGATTTACCTGGTATGCCGCCTAAAAGGGATATAGAGTTCAGAATAGATCTGGTGCCAGGAACAACTCTGATCCATAAGCGACCATATAGAAT
Reverse complement sequence
ATTCTATATGGTCGCTTATGGATCAGAGTTGTTCCTGGCACCAGATCTATTCTGAACTCTATATCCCTTTTAGGCGGCATACCAGGTAAATCATCAGGGA[A/G]
CACATCAGGGTACTCCCGGACTATAGGAATCTCTTCCAAAGTTATTTGGTTTAGACTTGACCTTCGAGGTTCAGAGGGCAATGCATGAACAGTTACAACT
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 | 67.50% | 0.80% | 2.14% | 29.60% | NA |
| All Indica | 2759 | 54.10% | 0.00% | 3.15% | 42.73% | NA |
| All Japonica | 1512 | 93.00% | 2.20% | 0.73% | 4.03% | NA |
| Aus | 269 | 48.70% | 0.40% | 0.37% | 50.56% | NA |
| Indica I | 595 | 59.50% | 0.20% | 1.18% | 39.16% | NA |
| Indica II | 465 | 60.60% | 0.00% | 3.23% | 36.13% | NA |
| Indica III | 913 | 41.90% | 0.00% | 5.15% | 52.90% | NA |
| Indica Intermediate | 786 | 60.20% | 0.00% | 2.29% | 37.53% | NA |
| Temperate Japonica | 767 | 96.10% | 1.60% | 0.91% | 1.43% | NA |
| Tropical Japonica | 504 | 96.20% | 0.40% | 0.20% | 3.17% | NA |
| Japonica Intermediate | 241 | 76.30% | 8.30% | 1.24% | 14.11% | NA |
| VI/Aromatic | 96 | 88.50% | 0.00% | 0.00% | 11.46% | NA |
| Intermediate | 90 | 83.30% | 1.10% | 2.22% | 13.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0714435734 | T -> DEL | LOC_Os07g25270.1 | N | frameshift_variant | Average:8.263; most accessible tissue: Callus, score: 36.188 | N | N | N | N |
| vg0714435734 | T -> C | LOC_Os07g25270.1 | missense_variant ; p.Phe113Leu; MODERATE | nonsynonymous_codon ; F113L | Average:8.263; most accessible tissue: Callus, score: 36.188 | benign  |
0.656 |
DELETERIOUS | 0.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0714435734 | 5.96E-06 | NA | mr1116 | 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 |
| vg0714435734 | 8.47E-07 | NA | mr1118 | 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 |
| vg0714435734 | 8.19E-07 | NA | mr1119 | 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 |
| vg0714435734 | 2.41E-08 | 1.05E-07 | mr1240 | 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 |
| vg0714435734 | 1.35E-06 | NA | mr1242 | 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 |
| vg0714435734 | 1.84E-07 | 2.24E-06 | mr1496 | 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 |
| vg0714435734 | 8.33E-08 | 4.91E-09 | mr1936 | 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 |