Search for Variation information by Variation ID:
Detailed information for vg1125736814:
| Variant ID: vg1125736814 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 25736814 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, G: 0.06, others allele: 0.00, population size: 81. )
Flanking Sequence (100 bp) in Reference Genome:
AAGGAGCAGCTCCTATGCTTGAGAAGATCATCTGGTCCTTCACCAAGATGAATTCTCTCTCAGGCATCGACAATCTCTCCAAACTGAAGGAGCTCGAGTT[C/G]
ATTGGTGACCTTGTCCCTGACCAGGTGAAGATAGATATTAACACACATAGAAAGCATCCTGTTCTTAACCACAAGCTGCCACAGCACCAAGACCAAGAAA
Reverse complement sequence
TTTCTTGGTCTTGGTGCTGTGGCAGCTTGTGGTTAAGAACAGGATGCTTTCTATGTGTGTTAATATCTATCTTCACCTGGTCAGGGACAAGGTCACCAAT[G/C]
AACTCGAGCTCCTTCAGTTTGGAGAGATTGTCGATGCCTGAGAGAGAATTCATCTTGGTGAAGGACCAGATGATCTTCTCAAGCATAGGAGCTGCTCCTT
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 | 60.10% | 29.20% | 2.75% | 8.02% | NA |
| All Indica | 2759 | 58.30% | 26.40% | 3.48% | 11.85% | NA |
| All Japonica | 1512 | 61.00% | 36.70% | 1.59% | 0.66% | NA |
| Aus | 269 | 71.70% | 24.20% | 1.86% | 2.23% | NA |
| Indica I | 595 | 40.50% | 51.60% | 3.53% | 4.37% | NA |
| Indica II | 465 | 59.80% | 32.50% | 2.80% | 4.95% | NA |
| Indica III | 913 | 65.10% | 13.10% | 3.07% | 18.73% | NA |
| Indica Intermediate | 786 | 63.00% | 19.10% | 4.33% | 13.61% | NA |
| Temperate Japonica | 767 | 40.20% | 58.00% | 1.43% | 0.39% | NA |
| Tropical Japonica | 504 | 86.90% | 10.70% | 1.59% | 0.79% | NA |
| Japonica Intermediate | 241 | 73.40% | 23.20% | 2.07% | 1.24% | NA |
| VI/Aromatic | 96 | 65.60% | 4.20% | 2.08% | 28.12% | NA |
| Intermediate | 90 | 57.80% | 28.90% | 3.33% | 10.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1125736814 | C -> DEL | LOC_Os11g42720.1 | N | frameshift_variant | Average:13.579; most accessible tissue: Callus, score: 41.293 | N | N | N | N |
| vg1125736814 | C -> G | LOC_Os11g42720.1 | missense_variant ; p.Phe1323Leu; MODERATE | nonsynonymous_codon ; F1323L | Average:13.579; most accessible tissue: Callus, score: 41.293 | benign  |
-0.186 |
TOLERATED | 0.28 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1125736814 | 1.41E-08 | 1.77E-13 | mr1191 | 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 |
| vg1125736814 | 4.45E-06 | 4.45E-06 | mr1597 | 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 |
| vg1125736814 | 3.25E-07 | 7.42E-10 | mr1644 | 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 |
| vg1125736814 | 2.54E-11 | 1.98E-17 | mr1644 | 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 |
| vg1125736814 | 1.75E-07 | NA | mr1191_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 |
| vg1125736814 | 6.58E-12 | 9.13E-22 | mr1191_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 |
| vg1125736814 | NA | 6.44E-06 | mr1530_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 |
| vg1125736814 | NA | 2.94E-09 | mr1745_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 |