Search for Variation information by Variation ID:
Detailed information for vg1216441109:
| Variant ID: vg1216441109 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 16441109 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 112. )
Flanking Sequence (100 bp) in Reference Genome:
CCCTGGCTTGCTTCCCTGTTCCTTCCTGACGGGCTGGTTCTGAGCTAGAGTTGCTGTAGGACGAGCAACCATGTTGCGGTTGTCATTGCCACGATTACCA[A/G]
TATTGTTGTTGTAAAACTGGCGTTGGGGGCGGATAACTGATGAAGATCCTCCTTGAGGGTACGATGGAGCTTGAGGTCCCGTAACGAGACGCGGCCTCTG
Reverse complement sequence
CAGAGGCCGCGTCTCGTTACGGGACCTCAAGCTCCATCGTACCCTCAAGGAGGATCTTCATCAGTTATCCGCCCCCAACGCCAGTTTTACAACAACAATA[T/C]
TGGTAATCGTGGCAATGACAACCGCAACATGGTTGCTCGTCCTACAGCAACTCTAGCTCAGAACCAGCCCGTCAGGAAGGAACAGGGAAGCAAGCCAGGG
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 | 13.20% | 4.00% | 71.84% | 10.98% | NA |
| All Indica | 2759 | 5.50% | 1.10% | 83.22% | 10.15% | NA |
| All Japonica | 1512 | 29.20% | 9.90% | 45.77% | 15.15% | NA |
| Aus | 269 | 4.50% | 0.70% | 94.05% | 0.74% | NA |
| Indica I | 595 | 3.20% | 0.20% | 72.44% | 24.20% | NA |
| Indica II | 465 | 9.50% | 1.30% | 87.74% | 1.51% | NA |
| Indica III | 913 | 4.10% | 1.30% | 88.17% | 6.46% | NA |
| Indica Intermediate | 786 | 6.60% | 1.50% | 82.95% | 8.91% | NA |
| Temperate Japonica | 767 | 51.40% | 11.20% | 25.55% | 11.86% | NA |
| Tropical Japonica | 504 | 1.60% | 3.00% | 73.21% | 22.22% | NA |
| Japonica Intermediate | 241 | 16.60% | 19.90% | 52.70% | 10.79% | NA |
| VI/Aromatic | 96 | 1.00% | 2.10% | 94.79% | 2.08% | NA |
| Intermediate | 90 | 17.80% | 5.60% | 70.00% | 6.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1216441109 | A -> DEL | LOC_Os12g27880.1 | N | frameshift_variant | Average:38.577; most accessible tissue: Minghui63 young leaf, score: 64.378 | N | N | N | N |
| vg1216441109 | A -> G | LOC_Os12g27880.1 | missense_variant ; p.Ile285Thr; MODERATE | nonsynonymous_codon ; I285T | Average:38.577; most accessible tissue: Minghui63 young leaf, score: 64.378 | possibly damaging  |
-1.528 |
TOLERATED | 0.69 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1216441109 | NA | 3.44E-06 | mr1010 | 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 |
| vg1216441109 | NA | 1.00E-08 | mr1163 | 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 |
| vg1216441109 | NA | 1.83E-07 | mr1010_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 |
| vg1216441109 | NA | 6.54E-06 | mr1182_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 |
| vg1216441109 | NA | 4.44E-06 | mr1588_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 |
| vg1216441109 | 2.64E-06 | NA | mr1670_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 |