Search for Variation information by Variation ID:
Detailed information for vg1000646158:
| Variant ID: vg1000646158 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 646158 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.87, C: 0.13, others allele: 0.00, population size: 63. )
Flanking Sequence (100 bp) in Reference Genome:
CCTACACCAGTCAACCTAACCCATTGCCACCGAAACAGAGGGACCTTGAGAGGTCCATAGTCAAGTTCCCATATCTCCTCGATGGCACCGTAATACGTGC[T/C]
AGTTGTACCATCGTGTCCCATGGCATCGATACGAACATCACTGTTCTGGTTCGTGCTTTTCATGTCTTGGGCTCTTGTGTAGAATGTGCACCCATTGATC
Reverse complement sequence
GATCAATGGGTGCACATTCTACACAAGAGCCCAAGACATGAAAAGCACGAACCAGAACAGTGATGTTCGTATCGATGCCATGGGACACGATGGTACAACT[A/G]
GCACGTATTACGGTGCCATCGAGGAGATATGGGAACTTGACTATGGACCTCTCAAGGTCCCTCTGTTTCGGTGGCAATGGGTTAGGTTGACTGGTGTAGG
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 | 19.70% | 0.70% | 29.12% | 50.51% | NA |
| All Indica | 2759 | 1.90% | 0.40% | 36.10% | 61.58% | NA |
| All Japonica | 1512 | 54.90% | 1.30% | 10.19% | 33.60% | NA |
| Aus | 269 | 5.90% | 0.00% | 46.10% | 47.96% | NA |
| Indica I | 595 | 2.00% | 1.00% | 39.66% | 57.31% | NA |
| Indica II | 465 | 1.90% | 0.40% | 15.91% | 81.72% | NA |
| Indica III | 913 | 0.90% | 0.00% | 44.36% | 54.76% | NA |
| Indica Intermediate | 786 | 2.90% | 0.50% | 35.75% | 60.81% | NA |
| Temperate Japonica | 767 | 87.20% | 0.00% | 0.91% | 11.86% | NA |
| Tropical Japonica | 504 | 8.70% | 3.80% | 24.60% | 62.90% | NA |
| Japonica Intermediate | 241 | 48.50% | 0.40% | 9.54% | 41.49% | NA |
| VI/Aromatic | 96 | 9.40% | 0.00% | 80.21% | 10.42% | NA |
| Intermediate | 90 | 25.60% | 1.10% | 27.78% | 45.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1000646158 | T -> C | LOC_Os10g02030.1 | missense_variant ; p.Ser715Gly; MODERATE | nonsynonymous_codon ; S715G | Average:4.91; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
-0.665 |
TOLERATED | 0.61 |
| vg1000646158 | T -> DEL | LOC_Os10g02030.1 | N | frameshift_variant | Average:4.91; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1000646158 | NA | 1.65E-08 | mr1716 | 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 |
| vg1000646158 | 2.09E-06 | 7.18E-06 | mr1716 | 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 |