Search for Variation information by Variation ID:
Detailed information for vg1000628143:
| Variant ID: vg1000628143 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 628143 |
| 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: 254. )
Flanking Sequence (100 bp) in Reference Genome:
TTGATGGTTACGAACAGCAGCGCTAGTAGGTTAAATTCCTCCTGTTTGTCTTCGTCCCACACGGGGACACCTTCCTTCTTCCATAATAGTTTAAGATCTT[C/T]
GACCAGTGGTCTTAGGAACACATCGATGTCGTTACCAGGTTGCTTGGGGCCTTGAATAATAATCGGCATCATTATGTACTTCCTCTTCATGCATAGCCAA
Reverse complement sequence
TTGGCTATGCATGAAGAGGAAGTACATAATGATGCCGATTATTATTCAAGGCCCCAAGCAACCTGGTAACGACATCGATGTGTTCCTAAGACCACTGGTC[G/A]
AAGATCTTAAACTATTATGGAAGAAGGAAGGTGTCCCCGTGTGGGACGAAGACAAACAGGAGGAATTTAACCTACTAGCGCTGCTGTTCGTAACCATCAA
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 | 81.00% | 17.70% | 1.29% | 0.00% | NA |
| All Indica | 2759 | 74.30% | 25.60% | 0.18% | 0.00% | NA |
| All Japonica | 1512 | 96.00% | 0.60% | 3.44% | 0.00% | NA |
| Aus | 269 | 57.60% | 42.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 56.80% | 43.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 94.00% | 6.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 73.50% | 26.20% | 0.33% | 0.00% | NA |
| Indica Intermediate | 786 | 76.70% | 23.00% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 93.20% | 0.30% | 6.52% | 0.00% | NA |
| Tropical Japonica | 504 | 98.60% | 1.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 94.80% | 2.10% | 3.12% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 5.60% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1000628143 | C -> T | LOC_Os10g01984.1 | missense_variant ; p.Glu384Lys; MODERATE | nonsynonymous_codon ; E384K | Average:24.107; most accessible tissue: Zhenshan97 panicle, score: 36.038 | benign  |
0.521 |
DELETERIOUS | 0.03 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1000628143 | NA | 2.01E-09 | mr1332_2 | 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 |
| vg1000628143 | NA | 2.00E-06 | mr1332_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 |
| vg1000628143 | NA | 5.98E-06 | mr1977_2 | 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 |