Search for Variation information by Variation ID:
Detailed information for vg0910046650:
| Variant ID: vg0910046650 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 10046650 |
| Reference Allele: T | Alternative Allele: C,A |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, C: 0.01, others allele: 0.00, population size: 100. )
Flanking Sequence (100 bp) in Reference Genome:
GGGCTGTTCTGGCAGAGCTGGCTGAACTGATTGAGCTAGAATCATTAGTGAACTCGGAGTAGGGTTGAGGCTGTGCTGCTCACTGTTGTTGTGACTGCCA[T/C,A]
TATGGTGGTTCTTGTTGAAGCTACCCGGGTGGTAGGGACGGTGCTGCCGGATAATCATGGTGGAAGGTCCACCCTGATGTCCCATCGTGAAACAAGGCTT
Reverse complement sequence
AAGCCTTGTTTCACGATGGGACATCAGGGTGGACCTTCCACCATGATTATCCGGCAGCACCGTCCCTACCACCCGGGTAGCTTCAACAAGAACCACCATA[A/G,T]
TGGCAGTCACAACAACAGTGAGCAGCACAGCCTCAACCCTACTCCGAGTTCACTAATGATTCTAGCTCAATCAGTTCAGCCAGCTCTGCCAGAACAGCCC
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 | 38.40% | 0.80% | 51.93% | 8.80% | A: 0.06% |
| All Indica | 2759 | 9.90% | 1.30% | 79.01% | 9.64% | A: 0.11% |
| All Japonica | 1512 | 90.50% | 0.10% | 4.10% | 5.22% | NA |
| Aus | 269 | 20.40% | 0.40% | 66.91% | 12.27% | NA |
| Indica I | 595 | 17.00% | 1.00% | 65.71% | 16.30% | NA |
| Indica II | 465 | 6.70% | 1.30% | 76.34% | 15.70% | NA |
| Indica III | 913 | 5.80% | 1.20% | 90.36% | 2.41% | A: 0.22% |
| Indica Intermediate | 786 | 11.30% | 1.70% | 77.48% | 9.41% | A: 0.13% |
| Temperate Japonica | 767 | 95.20% | 0.00% | 1.30% | 3.52% | NA |
| Tropical Japonica | 504 | 85.30% | 0.40% | 8.73% | 5.56% | NA |
| Japonica Intermediate | 241 | 86.70% | 0.00% | 3.32% | 9.96% | NA |
| VI/Aromatic | 96 | 64.60% | 0.00% | 7.29% | 28.12% | NA |
| Intermediate | 90 | 60.00% | 0.00% | 27.78% | 12.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0910046650 | T -> DEL | LOC_Os09g16430.1 | N | frameshift_variant | Average:18.362; most accessible tissue: Minghui63 root, score: 29.362 | N | N | N | N |
| vg0910046650 | T -> C | LOC_Os09g16430.1 | missense_variant ; p.Asn326Ser; MODERATE | nonsynonymous_codon | Average:18.362; most accessible tissue: Minghui63 root, score: 29.362 | benign  |
-0.291 |
TOLERATED | 0.84 |
| vg0910046650 | T -> A | LOC_Os09g16430.1 | missense_variant ; p.Asn326Ile; MODERATE | nonsynonymous_codon | Average:18.362; most accessible tissue: Minghui63 root, score: 29.362 | benign |
1.131 |
DELETERIOUS | 0.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0910046650 | 1.71E-06 | 1.57E-06 | mr1697 | Jap_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 |
| vg0910046650 | NA | 4.93E-06 | mr1006_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 |