Search for Variation information by Variation ID:
Detailed information for vg1005063902:
| Variant ID: vg1005063902 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 5063902 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AGCTTGGATTTTAGCTTCAGTGTCTTTGCGTTCTCGCCGTTTGGCCAGTTTTAACTTGGCTTTCTCCAATTTAAATTGATGTTGCTCAAGATAAACAGCT[A/G]
GAGTAAGGATATCAGCTAACTCGTCTGGGATCAGAGCTTGAATCTCATGTAGCCGAGTCCTAATTGACCCGCAATCAACTACCAAGCTATCTAGTGATGA
Reverse complement sequence
TCATCACTAGATAGCTTGGTAGTTGATTGCGGGTCAATTAGGACTCGGCTACATGAGATTCAAGCTCTGATCCCAGACGAGTTAGCTGATATCCTTACTC[T/C]
AGCTGTTTATCTTGAGCAACATCAATTTAAATTGGAGAAAGCCAAGTTAAAACTGGCCAAACGGCGAGAACGCAAAGACACTGAAGCTAAAATCCAAGCT
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 39.20% | 34.40% | 14.81% | 11.57% | NA |
| All Indica | 2759 | 54.40% | 17.50% | 22.80% | 5.26% | NA |
| All Japonica | 1512 | 5.70% | 67.70% | 1.39% | 25.26% | NA |
| Aus | 269 | 74.70% | 14.10% | 10.78% | 0.37% | NA |
| Indica I | 595 | 26.20% | 40.00% | 28.07% | 5.71% | NA |
| Indica II | 465 | 56.10% | 14.00% | 25.38% | 4.52% | NA |
| Indica III | 913 | 73.90% | 3.50% | 17.96% | 4.60% | NA |
| Indica Intermediate | 786 | 52.20% | 18.80% | 22.90% | 6.11% | NA |
| Temperate Japonica | 767 | 3.90% | 79.30% | 0.39% | 16.43% | NA |
| Tropical Japonica | 504 | 4.40% | 55.20% | 2.78% | 37.70% | NA |
| Japonica Intermediate | 241 | 14.10% | 56.80% | 1.66% | 27.39% | NA |
| VI/Aromatic | 96 | 36.50% | 40.60% | 8.33% | 14.58% | NA |
| Intermediate | 90 | 32.20% | 47.80% | 14.44% | 5.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1005063902 | A -> G | LOC_Os10g09390.1 | missense_variant ; p.Leu158Pro; MODERATE | nonsynonymous_codon ; L158P | Average:12.759; most accessible tissue: Callus, score: 31.236 | benign  |
-0.617 |
TOLERATED | 1.00 |
| vg1005063902 | A -> DEL | LOC_Os10g09390.1 | N | frameshift_variant | Average:12.759; most accessible tissue: Callus, score: 31.236 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1005063902 | NA | 6.69E-07 | mr1690 | 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 |
| vg1005063902 | 6.82E-07 | 2.73E-08 | mr1768_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 |
| vg1005063902 | NA | 2.44E-07 | mr1821_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 |