Search for Variation information by Variation ID:
Detailed information for vg1101998893:
| Variant ID: vg1101998893 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 1998893 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 286. )
Flanking Sequence (100 bp) in Reference Genome:
GCGGGTGAAGAACCATGGTCAAGCGAGGCCTCCGACGATGTCCCCGACACATCGCACATGTCGGACGAACAATTTCAACAGTTCATCGACCAGTACTGGG[C/G]
AGAGCAAGGATTCAACATTTGGAGTTGGATTCGTGCTTCCAGGACGTCGTCAAGCTCCACGCCGGGGCCAACCAGGCGGACGGCGGCGTCATGGCAGGCC
Reverse complement sequence
GGCCTGCCATGACGCCGCCGTCCGCCTGGTTGGCCCCGGCGTGGAGCTTGACGACGTCCTGGAAGCACGAATCCAACTCCAAATGTTGAATCCTTGCTCT[G/C]
CCCAGTACTGGTCGATGAACTGTTGAAATTGTTCGTCCGACATGTGCGATGTGTCGGGGACATCGTCGGAGGCCTCGCTTGACCATGGTTCTTCACCCGC
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.50% | 1.20% | 0.36% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 95.40% | 3.60% | 1.06% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 97.50% | 1.20% | 1.30% | 0.00% | NA |
| Tropical Japonica | 504 | 92.10% | 7.10% | 0.79% | 0.00% | NA |
| Japonica Intermediate | 241 | 95.40% | 3.70% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 1.10% | 1.11% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1101998893 | C -> G | LOC_Os11g04690.1 | missense_variant ; p.Ala35Gly; MODERATE | nonsynonymous_codon ; A35G | Average:63.529; most accessible tissue: Zhenshan97 panicle, score: 79.071 | benign  |
0.955 |
TOLERATED | 0.16 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1101998893 | NA | 1.89E-06 | mr1156 | 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 |
| vg1101998893 | NA | 4.74E-06 | mr1179 | 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 |
| vg1101998893 | NA | 3.40E-08 | mr1951 | 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 |