Search for Variation information by Variation ID:
Detailed information for vg1005203236:
| Variant ID: vg1005203236 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 5203236 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.67, A: 0.35, others allele: 0.00, population size: 55. )
Flanking Sequence (100 bp) in Reference Genome:
AGTTCCTGCTTTGCCATCACCGCTCATTCCACGTTTGCATGGACAATCATATCCGCCTGGTCTGTTCATGCAGATTCCATTTCTTGAACAAGGATACAGG[A/G]
CTCGGAGCTCAGGATGGCTATCTCGGAGGGCACATTCATCAATATCTGTGCGCAAACAGCAATTAATTTTCACATATCCGTGTACTCATGGTGTAATATT
Reverse complement sequence
AATATTACACCATGAGTACACGGATATGTGAAAATTAATTGCTGTTTGCGCACAGATATTGATGAATGTGCCCTCCGAGATAGCCATCCTGAGCTCCGAG[T/C]
CCTGTATCCTTGTTCAAGAAATGGAATCTGCATGAACAGACCAGGCGGATATGATTGTCCATGCAAACGTGGAATGAGCGGTGATGGCAAAGCAGGAACT
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 | 64.40% | 32.10% | 0.00% | 3.49% | NA |
| All Indica | 2759 | 89.10% | 10.50% | 0.00% | 0.40% | NA |
| All Japonica | 1512 | 16.00% | 75.90% | 0.00% | 8.13% | NA |
| Aus | 269 | 98.50% | 0.70% | 0.00% | 0.74% | NA |
| Indica I | 595 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 86.00% | 14.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 82.30% | 17.10% | 0.00% | 0.66% | NA |
| Indica Intermediate | 786 | 91.30% | 8.00% | 0.00% | 0.64% | NA |
| Temperate Japonica | 767 | 7.60% | 79.10% | 0.00% | 13.30% | NA |
| Tropical Japonica | 504 | 29.00% | 70.20% | 0.00% | 0.79% | NA |
| Japonica Intermediate | 241 | 15.80% | 77.20% | 0.00% | 7.05% | NA |
| VI/Aromatic | 96 | 30.20% | 46.90% | 0.00% | 22.92% | NA |
| Intermediate | 90 | 55.60% | 36.70% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1005203236 | A -> G | LOC_Os10g09620.1 | missense_variant ; p.Val326Ala; MODERATE | nonsynonymous_codon ; V326A | Average:47.809; most accessible tissue: Callus, score: 73.652 | benign  |
-0.16 |
TOLERATED | 0.74 |
| vg1005203236 | A -> DEL | LOC_Os10g09620.1 | N | frameshift_variant | Average:47.809; most accessible tissue: Callus, score: 73.652 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1005203236 | NA | 5.45E-07 | mr1278 | 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 |
| vg1005203236 | NA | 2.02E-09 | mr1368 | 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 |
| vg1005203236 | NA | 1.05E-08 | mr1658 | 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 |
| vg1005203236 | 9.30E-07 | NA | mr1758 | 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 |
| vg1005203236 | 6.64E-06 | 6.64E-06 | mr1758 | Jap_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 |
| vg1005203236 | NA | 7.84E-07 | mr1764 | 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 |
| vg1005203236 | NA | 7.97E-08 | mr1399_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 |
| vg1005203236 | NA | 4.26E-06 | mr1860_2 | Jap_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 |