Search for Variation information by Variation ID:
Detailed information for vg0202528514:
| Variant ID: vg0202528514 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 2528514 |
| 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: 241. )
Flanking Sequence (100 bp) in Reference Genome:
GTCCCCTTGAGATATCTGAGAATTTGCTTCACCGCCTTGAAATGCATCACTGTCGGTCGTTCCATGAATCTGCTCACCACGCCTACTGTGTAGGACAAAT[C/T]
CGGCCGAGTATGCAACAAGTAACGAAGACAACCTATCACTCGCCTGTACTCCGTGGGATCAACTGTGCTTCCTTGAGCATCTTTGTGCAACTGTGAACGA
Reverse complement sequence
TCGTTCACAGTTGCACAAAGATGCTCAAGGAAGCACAGTTGATCCCACGGAGTACAGGCGAGTGATAGGTTGTCTTCGTTACTTGTTGCATACTCGGCCG[G/A]
ATTTGTCCTACACAGTAGGCGTGGTGAGCAGATTCATGGAACGACCGACAGTGATGCATTTCAAGGCGGTGAAGCAAATTCTCAGATATCTCAAGGGGAC
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 | 82.50% | 0.70% | 5.69% | 11.15% | NA |
| All Indica | 2759 | 94.20% | 0.50% | 3.52% | 1.78% | NA |
| All Japonica | 1512 | 62.30% | 0.00% | 8.00% | 29.70% | NA |
| Aus | 269 | 71.70% | 2.20% | 17.84% | 8.18% | NA |
| Indica I | 595 | 94.30% | 0.30% | 2.35% | 3.03% | NA |
| Indica II | 465 | 99.40% | 0.00% | 0.65% | 0.00% | NA |
| Indica III | 913 | 90.70% | 0.00% | 6.90% | 2.41% | NA |
| Indica Intermediate | 786 | 95.30% | 1.40% | 2.16% | 1.15% | NA |
| Temperate Japonica | 767 | 92.00% | 0.00% | 4.95% | 3.00% | NA |
| Tropical Japonica | 504 | 19.60% | 0.00% | 9.52% | 70.83% | NA |
| Japonica Intermediate | 241 | 56.80% | 0.00% | 14.52% | 28.63% | NA |
| VI/Aromatic | 96 | 87.50% | 11.50% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 88.90% | 1.10% | 2.22% | 7.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0202528514 | C -> T | LOC_Os02g05260.1 | missense_variant ; p.Asp1126Asn; MODERATE | nonsynonymous_codon ; D1126N | Average:48.339; most accessible tissue: Zhenshan97 panicle, score: 59.59 | benign  |
1.069 |
DELETERIOUS | 0.03 |
| vg0202528514 | C -> DEL | LOC_Os02g05260.1 | N | frameshift_variant | Average:48.339; most accessible tissue: Zhenshan97 panicle, score: 59.59 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0202528514 | 1.29E-06 | 1.28E-06 | mr1978 | 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 |