Search for Variation information by Variation ID:
Detailed information for vg1208053849:
| Variant ID: vg1208053849 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 8053849 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.02, others allele: 0.00, population size: 107. )
Flanking Sequence (100 bp) in Reference Genome:
ATGCATCACCCAACATGTGTATCTCTCCATGAATCCCCGGCGTATCAAGTGAGCGTGTACTTCCTTTTCATCTTCCCACAAAATCTCTTTCCTGCAATCG[C/T]
TACATGGACAACACATGTACTTGTCGTTTCTTCTTATCCTATCCTCCTCTGCGGCTTTCATAAAACTTAATACGCCATCTCTATACTCTTTGTACTGACA
Reverse complement sequence
TGTCAGTACAAAGAGTATAGAGATGGCGTATTAAGTTTTATGAAAGCCGCAGAGGAGGATAGGATAAGAAGAAACGACAAGTACATGTGTTGTCCATGTA[G/A]
CGATTGCAGGAAAGAGATTTTGTGGGAAGATGAAAAGGAAGTACACGCTCACTTGATACGCCGGGGATTCATGGAGAGATACACATGTTGGGTGATGCAT
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 | 53.60% | 9.40% | 22.49% | 14.52% | NA |
| All Indica | 2759 | 51.30% | 14.70% | 27.73% | 6.27% | NA |
| All Japonica | 1512 | 55.80% | 0.40% | 10.98% | 32.80% | NA |
| Aus | 269 | 62.80% | 0.40% | 36.43% | 0.37% | NA |
| Indica I | 595 | 64.20% | 5.90% | 22.52% | 7.39% | NA |
| Indica II | 465 | 60.40% | 10.80% | 24.73% | 4.09% | NA |
| Indica III | 913 | 40.40% | 23.00% | 30.78% | 5.81% | NA |
| Indica Intermediate | 786 | 48.70% | 14.10% | 29.90% | 7.25% | NA |
| Temperate Japonica | 767 | 77.30% | 0.00% | 4.56% | 18.12% | NA |
| Tropical Japonica | 504 | 31.00% | 1.00% | 18.65% | 49.40% | NA |
| Japonica Intermediate | 241 | 39.40% | 0.40% | 15.35% | 44.81% | NA |
| VI/Aromatic | 96 | 53.10% | 26.00% | 16.67% | 4.17% | NA |
| Intermediate | 90 | 61.10% | 5.60% | 20.00% | 13.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1208053849 | C -> DEL | LOC_Os12g14180.1 | N | frameshift_variant | Average:15.422; most accessible tissue: Minghui63 flag leaf, score: 20.769 | N | N | N | N |
| vg1208053849 | C -> T | LOC_Os12g14180.1 | missense_variant ; p.Ser62Asn; MODERATE | nonsynonymous_codon ; S62N | Average:15.422; most accessible tissue: Minghui63 flag leaf, score: 20.769 | benign  |
1.428 |
TOLERATED | 0.46 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1208053849 | 1.09E-07 | 1.09E-07 | mr1342 | Ind_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 |
| vg1208053849 | 3.71E-06 | 5.26E-06 | mr1741 | Ind_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 |