Search for Variation information by Variation ID:
Detailed information for vg0414329989:
| Variant ID: vg0414329989 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 14329989 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.90, C: 0.10, others allele: 0.00, population size: 68. )
Flanking Sequence (100 bp) in Reference Genome:
GGTGTCATGAGCACCATCCTGGCGAATCCCGACGAGTTCTTGCTGACGACTTCGCTCGCGAAACTGGCGACGGCGATGGAGGTGATTCGCTCCAAGCATG[T/C]
GGCCAGGATCGGGGAGGAGACGTCCAACGGGATCTACACCGGGGCGTGCCACTTCCTCGCGTGCGTAAGGTTGTCGCACCCTGAACTCGATTTCCAGAGG
Reverse complement sequence
CCTCTGGAAATCGAGTTCAGGGTGCGACAACCTTACGCACGCGAGGAAGTGGCACGCCCCGGTGTAGATCCCGTTGGACGTCTCCTCCCCGATCCTGGCC[A/G]
CATGCTTGGAGCGAATCACCTCCATCGCCGTCGCCAGTTTCGCGAGCGAAGTCGTCAGCAAGAACTCGTCGGGATTCGCCAGGATGGTGCTCATGACACC
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 61.50% | 5.70% | 15.57% | 17.22% | NA |
| All Indica | 2759 | 51.50% | 4.50% | 18.48% | 25.48% | NA |
| All Japonica | 1512 | 90.40% | 0.20% | 3.24% | 6.15% | NA |
| Aus | 269 | 4.50% | 40.50% | 54.28% | 0.74% | NA |
| Indica I | 595 | 59.80% | 0.70% | 14.96% | 24.54% | NA |
| Indica II | 465 | 22.40% | 7.50% | 24.09% | 46.02% | NA |
| Indica III | 913 | 65.80% | 5.40% | 19.93% | 8.87% | NA |
| Indica Intermediate | 786 | 45.80% | 4.70% | 16.16% | 33.33% | NA |
| Temperate Japonica | 767 | 91.90% | 0.00% | 0.91% | 7.17% | NA |
| Tropical Japonica | 504 | 91.10% | 0.40% | 6.35% | 2.18% | NA |
| Japonica Intermediate | 241 | 84.20% | 0.40% | 4.15% | 11.20% | NA |
| VI/Aromatic | 96 | 54.20% | 26.00% | 17.71% | 2.08% | NA |
| Intermediate | 90 | 62.20% | 6.70% | 15.56% | 15.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0414329989 | T -> C | LOC_Os04g24860.1 | missense_variant ; p.Val200Ala; MODERATE | nonsynonymous_codon ; V200A | Average:11.561; most accessible tissue: Callus, score: 21.893 | benign  |
-1.222 |
TOLERATED | 1.00 |
| vg0414329989 | T -> DEL | LOC_Os04g24860.1 | N | frameshift_variant | Average:11.561; most accessible tissue: Callus, score: 21.893 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0414329989 | NA | 2.06E-07 | mr1343 | 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 |
| vg0414329989 | NA | 4.55E-10 | mr1722 | 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 |
| vg0414329989 | NA | 3.38E-06 | mr1322_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 |
| vg0414329989 | NA | 3.77E-06 | mr1364_2 | Ind_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 |