Search for Variation information by Variation ID:
Detailed information for vg1105311850:
| Variant ID: vg1105311850 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5311850 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 84. )
Flanking Sequence (100 bp) in Reference Genome:
CACGCCCGGAAGGCACGGAGACAAAGTTGTGAGAGGGAATGGTAAGTTTGCTGTAATCAAAAGGTATAGTAGCTCCCTTGTGTGGTGGAGTTCCCTTGCT[G/C]
CTTGCTTCATCTTCATTTCTATTTTCCCCGTTCTTTCCCCCTAAGTCTTCATCTTCAAAGCGGTGAAGCTTGAATCAAGAGCACTAGGCTCTGATACCAA
Reverse complement sequence
TTGGTATCAGAGCCTAGTGCTCTTGATTCAAGCTTCACCGCTTTGAAGATGAAGACTTAGGGGGAAAGAACGGGGAAAATAGAAATGAAGATGAAGCAAG[C/G]
AGCAAGGGAACTCCACCACACAAGGGAGCTACTATACCTTTTGATTACAGCAAACTTACCATTCCCTCTCACAACTTTGTCTCCGTGCCTTCCGGGCGTG
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 31.10% | 11.20% | 9.44% | 48.26% | NA |
| All Indica | 2759 | 36.80% | 0.60% | 9.28% | 53.39% | NA |
| All Japonica | 1512 | 26.00% | 33.30% | 11.11% | 29.56% | NA |
| Aus | 269 | 5.60% | 0.00% | 3.72% | 90.71% | NA |
| Indica I | 595 | 25.70% | 0.20% | 9.58% | 64.54% | NA |
| Indica II | 465 | 16.30% | 0.20% | 9.68% | 73.76% | NA |
| Indica III | 913 | 50.20% | 0.30% | 9.53% | 39.98% | NA |
| Indica Intermediate | 786 | 41.60% | 1.40% | 8.52% | 48.47% | NA |
| Temperate Japonica | 767 | 42.50% | 20.60% | 16.30% | 20.60% | NA |
| Tropical Japonica | 504 | 6.50% | 57.70% | 5.95% | 29.76% | NA |
| Japonica Intermediate | 241 | 14.10% | 22.80% | 5.39% | 57.68% | NA |
| VI/Aromatic | 96 | 18.80% | 0.00% | 1.04% | 80.21% | NA |
| Intermediate | 90 | 31.10% | 12.20% | 12.22% | 44.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105311850 | G -> DEL | LOC_Os11g09919.1 | N | frameshift_variant | Average:9.497; most accessible tissue: Callus, score: 19.884 | N | N | N | N |
| vg1105311850 | G -> C | LOC_Os11g09919.1 | missense_variant ; p.Ser787Arg; MODERATE | nonsynonymous_codon ; S787R | Average:9.497; most accessible tissue: Callus, score: 19.884 | benign  |
0.085 |
DELETERIOUS | 0.04 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1105311850 | NA | 1.66E-07 | mr1042 | 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 |
| vg1105311850 | 1.44E-06 | 1.44E-06 | mr1043 | Jap_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 |
| vg1105311850 | NA | 8.09E-07 | mr1269 | 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 |
| vg1105311850 | NA | 3.22E-06 | mr1912 | 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 |
| vg1105311850 | NA | 6.27E-07 | mr1990 | 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 |
| vg1105311850 | NA | 1.19E-11 | mr1097_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 |