Search for Variation information by Variation ID:
Detailed information for vg1004376825:
| Variant ID: vg1004376825 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 4376825 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.05, others allele: 0.00, population size: 107. )
Flanking Sequence (100 bp) in Reference Genome:
CCTATCTCATGATGTGAGAAAAACACTTGAAGACATCTCGCATCGGCTAGAAGCCTCTTCTTTAGACAGTTTGTTAGTTGACTGTGGGTCAATTAGGACA[C/T]
GACTGCATGAAGTTCAAGCTCTGATTCCCGAAGATTTGGCCGATGTCCTAATTCCAGCCGCTTATCTTGAGCAACATCAGTTCAAGCTAGAAAAAGCCAA
Reverse complement sequence
TTGGCTTTTTCTAGCTTGAACTGATGTTGCTCAAGATAAGCGGCTGGAATTAGGACATCGGCCAAATCTTCGGGAATCAGAGCTTGAACTTCATGCAGTC[G/A]
TGTCCTAATTGACCCACAGTCAACTAACAAACTGTCTAAAGAAGAGGCTTCTAGCCGATGCGAGATGTCTTCAAGTGTTTTTCTCACATCATGAGATAGG
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 | 40.30% | 16.10% | 0.63% | 42.98% | NA |
| All Indica | 2759 | 29.60% | 16.40% | 1.09% | 52.88% | NA |
| All Japonica | 1512 | 67.50% | 1.10% | 0.00% | 31.35% | NA |
| Aus | 269 | 1.50% | 93.30% | 0.00% | 5.20% | NA |
| Indica I | 595 | 35.80% | 42.40% | 0.84% | 21.01% | NA |
| Indica II | 465 | 34.80% | 10.50% | 1.29% | 53.33% | NA |
| Indica III | 913 | 20.40% | 3.40% | 1.20% | 75.03% | NA |
| Indica Intermediate | 786 | 32.60% | 15.40% | 1.02% | 51.02% | NA |
| Temperate Japonica | 767 | 89.20% | 0.30% | 0.00% | 10.56% | NA |
| Tropical Japonica | 504 | 32.70% | 2.00% | 0.00% | 65.28% | NA |
| Japonica Intermediate | 241 | 71.40% | 2.10% | 0.00% | 26.56% | NA |
| VI/Aromatic | 96 | 31.20% | 19.80% | 0.00% | 48.96% | NA |
| Intermediate | 90 | 37.80% | 21.10% | 0.00% | 41.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1004376825 | C -> T | LOC_Os10g08080.1 | stop_gained ; p.Arg727*; HIGH | nonsynonymous_codon ; R727W | Average:26.096; most accessible tissue: Zhenshan97 flag leaf, score: 45.537 | probably damaging  |
3.32 |
DELETERIOUS | 0.05 |
| vg1004376825 | C -> DEL | LOC_Os10g08080.1 | N | frameshift_variant | Average:26.096; most accessible tissue: Zhenshan97 flag leaf, score: 45.537 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1004376825 | 2.39E-06 | 5.01E-09 | mr1090 | 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 |
| vg1004376825 | 5.50E-06 | 9.80E-08 | mr1211 | 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 |
| vg1004376825 | NA | 1.70E-08 | mr1090_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 |
| vg1004376825 | NA | 2.75E-07 | mr1211_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 |