Search for Variation information by Variation ID:
Detailed information for vg0401649161:
| Variant ID: vg0401649161 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 1649161 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, C: 0.04, A: 0.01, others allele: 0.00, population size: 82. )
Flanking Sequence (100 bp) in Reference Genome:
CTTGAGTACCATGCTCGAGGTGCCTGTTTTAAACCATAAAGAGCCTTGTCTAACTTACATATATAATGTGGATAGGCCTTATCTTCATGCCCTGGTGGTT[G/C]
ACGCATGTAGACCTCTACCTCCAGAACTCCATGAAGGAATGCGTTCTGTACATCCAATTGGCGAAGGCTCCAACCTTTTGAGACTGCAATAGACAGAATG
Reverse complement sequence
CATTCTGTCTATTGCAGTCTCAAAAGGTTGGAGCCTTCGCCAATTGGATGTACAGAACGCATTCCTTCATGGAGTTCTGGAGGTAGAGGTCTACATGCGT[C/G]
AACCACCAGGGCATGAAGATAAGGCCTATCCACATTATATATGTAAGTTAGACAAGGCTCTTTATGGTTTAAAACAGGCACCTCGAGCATGGTACTCAAG
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 | 37.80% | 0.30% | 26.26% | 35.72% | NA |
| All Indica | 2759 | 30.70% | 0.30% | 30.84% | 38.09% | NA |
| All Japonica | 1512 | 54.40% | 0.20% | 16.14% | 29.23% | NA |
| Aus | 269 | 14.10% | 0.00% | 37.92% | 47.96% | NA |
| Indica I | 595 | 36.30% | 0.20% | 38.99% | 24.54% | NA |
| Indica II | 465 | 53.30% | 0.20% | 16.34% | 30.11% | NA |
| Indica III | 913 | 9.60% | 0.30% | 35.05% | 54.98% | NA |
| Indica Intermediate | 786 | 37.70% | 0.50% | 28.37% | 33.46% | NA |
| Temperate Japonica | 767 | 84.50% | 0.10% | 3.39% | 11.99% | NA |
| Tropical Japonica | 504 | 21.20% | 0.40% | 26.59% | 51.79% | NA |
| Japonica Intermediate | 241 | 28.20% | 0.00% | 34.85% | 36.93% | NA |
| VI/Aromatic | 96 | 36.50% | 0.00% | 16.67% | 46.88% | NA |
| Intermediate | 90 | 45.60% | 0.00% | 31.11% | 23.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0401649161 | G -> C | LOC_Os04g03720.1 | missense_variant ; p.Gln396Glu; MODERATE | nonsynonymous_codon ; Q396E | Average:11.946; most accessible tissue: Callus, score: 24.66 | benign  |
0.748 |
DELETERIOUS | 0.00 |
| vg0401649161 | G -> DEL | LOC_Os04g03720.1 | N | frameshift_variant | Average:11.946; most accessible tissue: Callus, score: 24.66 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0401649161 | NA | 8.24E-07 | 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 |
| vg0401649161 | NA | 6.03E-06 | mr1164 | 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 |
| vg0401649161 | NA | 4.99E-07 | 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 |
| vg0401649161 | 2.96E-06 | 2.96E-06 | mr1663 | 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 |
| vg0401649161 | NA | 2.18E-06 | mr1689_2 | 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 |