Search for Variation information by Variation ID:
Detailed information for vg1209943592:
| Variant ID: vg1209943592 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 9943592 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 54. )
Flanking Sequence (100 bp) in Reference Genome:
ACTTCTCTGATTATTCGAACAGACCAAGCAAGCCTCAAATACATTAATGAGCAACGCCTTACAAAAGGGATTCAACATAAATTGCTAATCAAGCTCCTCA[A/G]
CTACAATTACAAAATAGAGTACAAGAAAGGCAAAGAAAACAAGGCTGCTGATGCCTTATCTCGCATACCTTTTGTTGCTCAGTGGTTTTCTACCACTATT
Reverse complement sequence
AATAGTGGTAGAAAACCACTGAGCAACAAAAGGTATGCGAGATAAGGCATCAGCAGCCTTGTTTTCTTTGCCTTTCTTGTACTCTATTTTGTAATTGTAG[T/C]
TGAGGAGCTTGATTAGCAATTTATGTTGAATCCCTTTTGTAAGGCGTTGCTCATTAATGTATTTGAGGCTTGCTTGGTCTGTTCGAATAATCAGAGAAGT
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 29.10% | 13.90% | 0.87% | 56.16% | NA |
| All Indica | 2759 | 7.10% | 21.30% | 1.20% | 70.35% | NA |
| All Japonica | 1512 | 73.90% | 3.00% | 0.07% | 22.95% | NA |
| Aus | 269 | 4.50% | 1.50% | 1.86% | 92.19% | NA |
| Indica I | 595 | 8.10% | 22.90% | 0.84% | 68.24% | NA |
| Indica II | 465 | 14.80% | 15.30% | 1.08% | 68.82% | NA |
| Indica III | 913 | 2.80% | 24.40% | 1.10% | 71.63% | NA |
| Indica Intermediate | 786 | 6.70% | 20.20% | 1.65% | 71.37% | NA |
| Temperate Japonica | 767 | 82.70% | 2.90% | 0.00% | 14.47% | NA |
| Tropical Japonica | 504 | 68.30% | 0.20% | 0.20% | 31.35% | NA |
| Japonica Intermediate | 241 | 58.10% | 9.50% | 0.00% | 32.37% | NA |
| VI/Aromatic | 96 | 10.40% | 9.40% | 0.00% | 80.21% | NA |
| Intermediate | 90 | 43.30% | 8.90% | 2.22% | 45.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1209943592 | A -> DEL | LOC_Os12g17360.1 | N | frameshift_variant | Average:35.2; most accessible tissue: Minghui63 young leaf, score: 68.07 | N | N | N | N |
| vg1209943592 | A -> G | LOC_Os12g17360.1 | missense_variant ; p.Asn213Ser; MODERATE | nonsynonymous_codon | Average:35.2; most accessible tissue: Minghui63 young leaf, score: 68.07 | benign  |
-0.068 |
TOLERATED | 0.20 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1209943592 | 1.36E-06 | 3.64E-07 | mr1337 | 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 |
| vg1209943592 | 5.76E-07 | NA | mr1526 | 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 |
| vg1209943592 | NA | 3.69E-06 | mr1312_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 |
| vg1209943592 | 2.34E-06 | 2.34E-06 | mr1312_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 |
| vg1209943592 | NA | 1.53E-06 | mr1371_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 |
| vg1209943592 | NA | 8.04E-06 | mr1833_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 |