Search for Variation information by Variation ID:
Detailed information for vg0142227444:
| Variant ID: vg0142227444 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 42227444 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.02, others allele: 0.00, population size: 291. )
Flanking Sequence (100 bp) in Reference Genome:
AGGGGCCAGGAATGCTCGCTCTCCTGGTGTGAAAAGCCAACGAAGCAAACCATCAGGCCGCAATGGTGATAGAACTAATTTCAAATCCAAATCTGAACCA[C/T]
GGCCAGGAAATGGCCAAAATACCAAGGGCGACAAACCTCAAGGTTTCAACAAAAGAAACAGAACTGGTAAGTTCGACAAGACACAAAATCGTGGGGGTAA
Reverse complement sequence
TTACCCCCACGATTTTGTGTCTTGTCGAACTTACCAGTTCTGTTTCTTTTGTTGAAACCTTGAGGTTTGTCGCCCTTGGTATTTTGGCCATTTCCTGGCC[G/A]
TGGTTCAGATTTGGATTTGAAATTAGTTCTATCACCATTGCGGCCTGATGGTTTGCTTCGTTGGCTTTTCACACCAGGAGAGCGAGCATTCCTGGCCCCT
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 | 66.70% | 33.00% | 0.30% | 0.00% | NA |
| All Indica | 2759 | 87.10% | 12.60% | 0.36% | 0.00% | NA |
| All Japonica | 1512 | 32.80% | 66.90% | 0.26% | 0.00% | NA |
| Aus | 269 | 40.10% | 59.90% | 0.00% | 0.00% | NA |
| Indica I | 595 | 90.30% | 9.40% | 0.34% | 0.00% | NA |
| Indica II | 465 | 96.60% | 3.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 82.60% | 17.20% | 0.22% | 0.00% | NA |
| Indica Intermediate | 786 | 84.20% | 15.00% | 0.76% | 0.00% | NA |
| Temperate Japonica | 767 | 7.80% | 92.00% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 53.00% | 46.40% | 0.60% | 0.00% | NA |
| Japonica Intermediate | 241 | 70.10% | 29.90% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 60.00% | 40.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0142227444 | C -> T | LOC_Os01g72780.1 | missense_variant ; p.Arg1126Trp; MODERATE | nonsynonymous_codon ; R1126W | Average:69.395; most accessible tissue: Callus, score: 86.521 | possibly damaging  |
1.84 |
TOLERATED | 0.08 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0142227444 | NA | 4.67E-06 | mr1509_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 |
| vg0142227444 | NA | 5.24E-06 | mr1544_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 |
| vg0142227444 | 3.75E-06 | NA | mr1629_2 | 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 |
| vg0142227444 | 6.74E-06 | NA | mr1676_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 |
| vg0142227444 | NA | 2.36E-06 | mr1676_2 | Ind_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 |
| vg0142227444 | NA | 3.98E-07 | mr1722_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 |