Search for Variation information by Variation ID:
Detailed information for vg0100695189:
| Variant ID: vg0100695189 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 695189 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, T: 0.00, others allele: 0.00, population size: 254. )
Flanking Sequence (100 bp) in Reference Genome:
ACAATTACCCATATGGAATCATGTCCTTTCTGCGTCCTGGGTAAGCCAACTACAAAGTCCATACCAATCTCATCCCATTTCCACACTGGGATGGGTAGAG[G/T]
TTGTAATAATCCAGCTAGCTTCCGATGTTCCGCTTTAATCCTTTGACAAGTATCGCAATGAGCGACAAACTGCGCAATGTCGGCTTTCATCCCATTCCAC
Reverse complement sequence
GTGGAATGGGATGAAAGCCGACATTGCGCAGTTTGTCGCTCATTGCGATACTTGTCAAAGGATTAAAGCGGAACATCGGAAGCTAGCTGGATTATTACAA[C/A]
CTCTACCCATCCCAGTGTGGAAATGGGATGAGATTGGTATGGACTTTGTAGTTGGCTTACCCAGGACGCAGAAAGGACATGATTCCATATGGGTAATTGT
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 74.40% | 9.10% | 1.71% | 14.75% | NA |
| All Indica | 2759 | 94.00% | 0.90% | 0.58% | 4.53% | NA |
| All Japonica | 1512 | 44.80% | 19.90% | 2.18% | 33.07% | NA |
| Aus | 269 | 51.70% | 24.90% | 7.06% | 16.36% | NA |
| Indica I | 595 | 96.00% | 0.00% | 0.34% | 3.70% | NA |
| Indica II | 465 | 95.50% | 2.20% | 0.00% | 2.37% | NA |
| Indica III | 913 | 94.70% | 0.10% | 0.44% | 4.71% | NA |
| Indica Intermediate | 786 | 90.70% | 1.80% | 1.27% | 6.23% | NA |
| Temperate Japonica | 767 | 70.40% | 21.60% | 0.65% | 7.30% | NA |
| Tropical Japonica | 504 | 7.30% | 13.50% | 4.17% | 75.00% | NA |
| Japonica Intermediate | 241 | 41.90% | 27.80% | 2.90% | 27.39% | NA |
| VI/Aromatic | 96 | 41.70% | 28.10% | 9.38% | 20.83% | NA |
| Intermediate | 90 | 74.40% | 12.20% | 4.44% | 8.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0100695189 | G -> T | LOC_Os01g02260.1 | missense_variant ; p.Pro238Thr; MODERATE | nonsynonymous_codon ; P238T | Average:36.053; most accessible tissue: Minghui63 root, score: 59.984 | benign  |
1.014 |
DELETERIOUS | 0.00 |
| vg0100695189 | G -> DEL | LOC_Os01g02260.1 | N | frameshift_variant | Average:36.053; most accessible tissue: Minghui63 root, score: 59.984 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0100695189 | 3.62E-07 | NA | Grain_weight | All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg0100695189 | 9.23E-06 | NA | mr1336 | 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 |
| vg0100695189 | 2.03E-06 | 2.03E-06 | mr1336 | 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 |