Search for Variation information by Variation ID:
Detailed information for vg0105865757:
| Variant ID: vg0105865757 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 5865757 |
| 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: 86. )
Flanking Sequence (100 bp) in Reference Genome:
TCTCGCCATGCCGCGGGCGATGCGTCGTCGCTGCCAATCCTGCGCACTGCCAGCACGGCGCCGTCGTCCAGCACCGCCATGTACACGATGCTGCTGCCCG[C/T]
CGCGCCCAGGATGTACGCCGACGCCTTCAGTAGCGTCTTCATCTCCAGCTCCACGTCGCCATCCACCGTCACCAGCACCGCGCCGCCGCCGCCACCATCC
Reverse complement sequence
GGATGGTGGCGGCGGCGGCGCGGTGCTGGTGACGGTGGATGGCGACGTGGAGCTGGAGATGAAGACGCTACTGAAGGCGTCGGCGTACATCCTGGGCGCG[G/A]
CGGGCAGCAGCATCGTGTACATGGCGGTGCTGGACGACGGCGCCGTGCTGGCAGTGCGCAGGATTGGCAGCGACGACGCATCGCCCGCGGCATGGCGAGA
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 | 91.50% | 1.20% | 7.28% | 0.02% | NA |
| All Indica | 2759 | 93.20% | 0.70% | 6.09% | 0.04% | NA |
| All Japonica | 1512 | 85.80% | 2.60% | 11.57% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 93.10% | 1.30% | 5.55% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.20% | 0.10% | 1.53% | 0.11% | NA |
| Indica Intermediate | 786 | 83.30% | 1.30% | 15.39% | 0.00% | NA |
| Temperate Japonica | 767 | 96.70% | 0.40% | 2.87% | 0.00% | NA |
| Tropical Japonica | 504 | 75.80% | 6.00% | 18.25% | 0.00% | NA |
| Japonica Intermediate | 241 | 72.20% | 2.50% | 25.31% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 1.10% | 1.11% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0105865757 | C -> T | LOC_Os01g11000.1 | missense_variant ; p.Ala171Thr; MODERATE | nonsynonymous_codon ; A171T | Average:48.627; most accessible tissue: Minghui63 panicle, score: 74.563 | benign  |
-0.043 |
TOLERATED | 0.11 |
| vg0105865757 | C -> DEL | LOC_Os01g11000.1 | N | frameshift_variant | Average:48.627; most accessible tissue: Minghui63 panicle, score: 74.563 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0105865757 | NA | 4.49E-06 | mr1077_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 |
| vg0105865757 | NA | 4.99E-07 | mr1243_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 |
| vg0105865757 | 8.05E-06 | 2.43E-08 | mr1248_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 |
| vg0105865757 | NA | 8.24E-08 | mr1250_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 |
| vg0105865757 | 8.46E-07 | 5.30E-10 | mr1800_2 | 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 |