Search for Variation information by Variation ID:
Detailed information for vg1209055808:
| Variant ID: vg1209055808 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 9055808 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, T: 0.03, others allele: 0.00, population size: 72. )
Flanking Sequence (100 bp) in Reference Genome:
TGGTCTATCTCCGCCGAAGTCCTCCGAGAATGAGCGAACCCTTCACGGAGAAACTCGAGGTGCAGCTGCGGACGATGATCTCGTATGCAAGCCAACACAT[G/T]
CCCTCCGGCATATCGGCTCAACCGACGGCATTCCTGCTTTAGGGCTTCGTCAATGCGCTTGCCGATGCCTTCGAGCTGAGTACATGCCCCATTCAGCCAC
Reverse complement sequence
GTGGCTGAATGGGGCATGTACTCAGCTCGAAGGCATCGGCAAGCGCATTGACGAAGCCCTAAAGCAGGAATGCCGTCGGTTGAGCCGATATGCCGGAGGG[C/A]
ATGTGTTGGCTTGCATACGAGATCATCGTCCGCAGCTGCACCTCGAGTTTCTCCGTGAAGGGTTCGCTCATTCTCGGAGGACTTCGGCGGAGATAGACCA
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 75.20% | 12.80% | 2.92% | 9.10% | NA |
| All Indica | 2759 | 60.40% | 20.00% | 4.71% | 14.90% | NA |
| All Japonica | 1512 | 98.50% | 0.40% | 0.13% | 0.93% | NA |
| Aus | 269 | 83.30% | 15.20% | 1.49% | 0.00% | NA |
| Indica I | 595 | 44.90% | 13.40% | 4.03% | 37.65% | NA |
| Indica II | 465 | 61.30% | 13.30% | 5.81% | 19.57% | NA |
| Indica III | 913 | 66.50% | 26.90% | 4.82% | 1.75% | NA |
| Indica Intermediate | 786 | 64.60% | 20.70% | 4.45% | 10.18% | NA |
| Temperate Japonica | 767 | 98.20% | 0.50% | 0.26% | 1.04% | NA |
| Tropical Japonica | 504 | 99.20% | 0.20% | 0.00% | 0.60% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.40% | 0.00% | 1.24% | NA |
| VI/Aromatic | 96 | 94.80% | 1.00% | 2.08% | 2.08% | NA |
| Intermediate | 90 | 92.20% | 4.40% | 0.00% | 3.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1209055808 | G -> DEL | LOC_Os12g15910.1 | N | frameshift_variant | Average:27.049; most accessible tissue: Minghui63 young leaf, score: 61.887 | N | N | N | N |
| vg1209055808 | G -> T | LOC_Os12g15910.1 | missense_variant ; p.His712Asn; MODERATE | nonsynonymous_codon ; H712N | Average:27.049; most accessible tissue: Minghui63 young leaf, score: 61.887 | benign  |
1.278 |
DELETERIOUS | 0.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1209055808 | 9.62E-07 | 3.22E-07 | mr1092 | 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 |