Search for Variation information by Variation ID:
Detailed information for vg0906525065:
| Variant ID: vg0906525065 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 6525065 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 112. )
Flanking Sequence (100 bp) in Reference Genome:
ATCAATGGGGCAGGTGGTTTCGTCCTGAGTTTGCATGGCGTCCATGCTCTGTGATCCTACCTGCCCCGTTGAGGCACAGCTACTACGATTGCCTGAGGGG[C/T]
TGACCATGATAGGAGGAATGTATGGCTGGGGATCCTGGCTCCGATATGCGGCCATGCGTTCATCCACCTTTCTTGCCACCTCCTCTTGCATGCTAAGCTC
Reverse complement sequence
GAGCTTAGCATGCAAGAGGAGGTGGCAAGAAAGGTGGATGAACGCATGGCCGCATATCGGAGCCAGGATCCCCAGCCATACATTCCTCCTATCATGGTCA[G/A]
CCCCTCAGGCAATCGTAGTAGCTGTGCCTCAACGGGGCAGGTAGGATCACAGAGCATGGACGCCATGCAAACTCAGGACGAAACCACCTGCCCCATTGAT
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 | 52.00% | 22.40% | 6.73% | 18.83% | NA |
| All Indica | 2759 | 25.00% | 32.10% | 11.09% | 31.86% | NA |
| All Japonica | 1512 | 99.10% | 0.50% | 0.13% | 0.20% | NA |
| Aus | 269 | 60.20% | 39.00% | 0.74% | 0.00% | NA |
| Indica I | 595 | 31.90% | 4.40% | 10.42% | 53.28% | NA |
| Indica II | 465 | 17.80% | 54.00% | 8.39% | 19.78% | NA |
| Indica III | 913 | 20.70% | 36.60% | 15.33% | 27.38% | NA |
| Indica Intermediate | 786 | 28.90% | 34.90% | 8.27% | 27.99% | NA |
| Temperate Japonica | 767 | 99.30% | 0.40% | 0.13% | 0.13% | NA |
| Tropical Japonica | 504 | 99.00% | 0.40% | 0.20% | 0.40% | NA |
| Japonica Intermediate | 241 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 56.20% | 42.70% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 60.00% | 23.30% | 7.78% | 8.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0906525065 | C -> DEL | LOC_Os09g11690.1 | N | frameshift_variant | Average:40.52; most accessible tissue: Minghui63 young leaf, score: 80.562 | N | N | N | N |
| vg0906525065 | C -> T | LOC_Os09g11690.1 | missense_variant ; p.Ser169Asn; MODERATE | nonsynonymous_codon ; S169N | Average:40.52; most accessible tissue: Minghui63 young leaf, score: 80.562 | benign  |
1.386 |
DELETERIOUS | 0.01 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0906525065 | NA | 8.32E-07 | mr1169_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 |
| vg0906525065 | NA | 7.61E-06 | mr1169_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 |
| vg0906525065 | NA | 2.70E-07 | mr1842_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 |
| vg0906525065 | 2.59E-07 | 2.59E-07 | mr1947_2 | 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 |