Search for Variation information by Variation ID:
Detailed information for vg1208012200:
| Variant ID: vg1208012200 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 8012200 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 268. )
Flanking Sequence (100 bp) in Reference Genome:
GGGTATGAACTTCTTTAGCCAGTTCACCTGCCCCGTGGCCTCATAGCATGCTATAAACTCGACATACATAGTAGACCCTCCAGTGATAGTCTGTTTTGAG[C/A]
TTTTCCATGAAATAGCTCCTCCTGCAAGGGTGAACACGTATCCCGATGTTGACTTTGCATTATCTTTTGCAAAATCAGAATCTGAATACCCCACTATCTG
Reverse complement sequence
CAGATAGTGGGGTATTCAGATTCTGATTTTGCAAAAGATAATGCAAAGTCAACATCGGGATACGTGTTCACCCTTGCAGGAGGAGCTATTTCATGGAAAA[G/T]
CTCAAAACAGACTATCACTGGAGGGTCTACTATGTATGTCGAGTTTATAGCATGCTATGAGGCCACGGGGCAGGTGAACTGGCTAAAGAAGTTCATACCC
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 83.60% | 5.90% | 0.80% | 9.63% | NA |
| All Indica | 2759 | 88.80% | 3.30% | 1.05% | 6.92% | NA |
| All Japonica | 1512 | 82.30% | 0.30% | 0.60% | 16.73% | NA |
| Aus | 269 | 34.60% | 65.10% | 0.00% | 0.37% | NA |
| Indica I | 595 | 81.30% | 5.00% | 2.86% | 10.76% | NA |
| Indica II | 465 | 93.10% | 1.50% | 0.00% | 5.38% | NA |
| Indica III | 913 | 91.20% | 2.10% | 0.66% | 6.02% | NA |
| Indica Intermediate | 786 | 88.90% | 4.30% | 0.76% | 5.98% | NA |
| Temperate Japonica | 767 | 82.70% | 0.30% | 0.39% | 16.69% | NA |
| Tropical Japonica | 504 | 92.50% | 0.20% | 0.20% | 7.14% | NA |
| Japonica Intermediate | 241 | 60.20% | 0.80% | 2.07% | 36.93% | NA |
| VI/Aromatic | 96 | 89.60% | 5.20% | 0.00% | 5.21% | NA |
| Intermediate | 90 | 88.90% | 5.60% | 0.00% | 5.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1208012200 | C -> DEL | LOC_Os12g14120.1 | N | frameshift_variant | Average:44.371; most accessible tissue: Zhenshan97 flag leaf, score: 63.101 | N | N | N | N |
| vg1208012200 | C -> A | LOC_Os12g14120.1 | missense_variant ; p.Ser625Ile; MODERATE | nonsynonymous_codon ; S625F | Average:44.371; most accessible tissue: Zhenshan97 flag leaf, score: 63.101 | probably damaging  |
2.788 |
DELETERIOUS | 0.01 |
| vg1208012200 | C -> A | LOC_Os12g14120.1 | missense_variant ; p.Ser625Ile; MODERATE | nonsynonymous_codon ; S625I | Average:44.371; most accessible tissue: Zhenshan97 flag leaf, score: 63.101 | probably damaging |
2.506 |
DELETERIOUS | 0.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1208012200 | 3.45E-09 | NA | mr1244_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 |
| vg1208012200 | NA | 5.15E-06 | mr1265_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 |
| vg1208012200 | NA | 8.41E-27 | mr1757_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 |
| vg1208012200 | NA | 6.44E-06 | mr1977_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 |