Search for Variation information by Variation ID:
Detailed information for vg1121619953:
| Variant ID: vg1121619953 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 21619953 |
| 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: 277. )
Flanking Sequence (100 bp) in Reference Genome:
TCCTCGCTGTTGATGAATTTGATTAGTGGGATGCGCCAGTCGTCTGTGGTCTCGATATCGGCAACGGCGCGTTCTGCCTTGGTGACCTCCGAGCTAATGT[C/T]
GGGGGTGTCCGGGCTAACTTCGCCGCTGACCTCTTTCACTGATGGCTTCGTCAGGATGTCGAGAAAAGTGCCGGGCTCGAGCGGTTCTCGTCTGGACGCA
Reverse complement sequence
TGCGTCCAGACGAGAACCGCTCGAGCCCGGCACTTTTCTCGACATCCTGACGAAGCCATCAGTGAAAGAGGTCAGCGGCGAAGTTAGCCCGGACACCCCC[G/A]
ACATTAGCTCGGAGGTCACCAAGGCAGAACGCGCCGTTGCCGATATCGAGACCACAGACGACTGGCGCATCCCACTAATCAAATTCATCAACAGCGAGGA
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 | 89.00% | 4.50% | 1.35% | 5.18% | NA |
| All Indica | 2759 | 99.50% | 0.10% | 0.25% | 0.11% | NA |
| All Japonica | 1512 | 67.50% | 13.40% | 3.37% | 15.74% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.37% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.00% | 0.17% | NA |
| Indica II | 465 | 99.10% | 0.20% | 0.65% | 0.00% | NA |
| Indica III | 913 | 99.20% | 0.30% | 0.33% | 0.11% | NA |
| Indica Intermediate | 786 | 99.70% | 0.00% | 0.13% | 0.13% | NA |
| Temperate Japonica | 767 | 91.00% | 1.20% | 0.65% | 7.17% | NA |
| Tropical Japonica | 504 | 37.90% | 30.80% | 7.74% | 23.61% | NA |
| Japonica Intermediate | 241 | 54.40% | 16.20% | 2.90% | 26.56% | NA |
| VI/Aromatic | 96 | 96.90% | 2.10% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 86.70% | 4.40% | 4.44% | 4.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1121619953 | C -> T | LOC_Os11g36640.1 | missense_variant ; p.Asp1451Asn; MODERATE | nonsynonymous_codon ; D1451N | Average:38.207; most accessible tissue: Minghui63 young leaf, score: 61.007 | benign  |
0.601 |
TOLERATED | 0.19 |
| vg1121619953 | C -> DEL | LOC_Os11g36640.1 | N | frameshift_variant | Average:38.207; most accessible tissue: Minghui63 young leaf, score: 61.007 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1121619953 | 4.70E-06 | NA | mr1178_2 | 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 |