Search for Variation information by Variation ID:
Detailed information for vg0805653724:
| Variant ID: vg0805653724 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 5653724 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, C: 0.04, others allele: 0.00, population size: 236. )
Flanking Sequence (100 bp) in Reference Genome:
GGGGTCACTCACACTGGATGCAGCCACTATCGTGCTTGATGATTCGTTTCTATATGCTGGTTATGAATACGAGTATGAAGACATCGATGAGGATGCGATC[G/C]
AAGGAAACGGTAGCGAAGACGGTGAAGGTTCCTTGAATGATTCTGACTACGACAGTGATGCTGTCAGTGATGCAAGTACCTGTGAATACAGTGAGATTGC
Reverse complement sequence
GCAATCTCACTGTATTCACAGGTACTTGCATCACTGACAGCATCACTGTCGTAGTCAGAATCATTCAAGGAACCTTCACCGTCTTCGCTACCGTTTCCTT[C/G]
GATCGCATCCTCATCGATGTCTTCATACTCGTATTCATAACCAGCATATAGAAACGAATCATCAAGCACGATAGTGGCTGCATCCAGTGTGAGTGACCCC
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 81.40% | 18.20% | 0.17% | 0.23% | NA |
| All Indica | 2759 | 73.30% | 26.20% | 0.18% | 0.36% | NA |
| All Japonica | 1512 | 99.70% | 0.30% | 0.00% | 0.07% | NA |
| Aus | 269 | 55.00% | 45.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 55.00% | 44.00% | 0.50% | 0.50% | NA |
| Indica II | 465 | 91.80% | 7.70% | 0.00% | 0.43% | NA |
| Indica III | 913 | 74.00% | 26.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 75.30% | 23.80% | 0.25% | 0.64% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 90.60% | 7.30% | 2.08% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 6.70% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0805653724 | G -> C | LOC_Os08g09780.1 | missense_variant ; p.Glu103Gln; MODERATE | nonsynonymous_codon ; E103Q | Average:62.38; most accessible tissue: Zhenshan97 young leaf, score: 79.507 | benign  |
0.506 |
TOLERATED | 0.07 |
| vg0805653724 | G -> C | LOC_Os08g09780.2 | missense_variant ; p.Glu103Gln; MODERATE | nonsynonymous_codon ; E103Q | Average:62.38; most accessible tissue: Zhenshan97 young leaf, score: 79.507 | benign |
0.506 |
TOLERATED | 0.06 |
| vg0805653724 | G -> DEL | LOC_Os08g09780.1 | N | frameshift_variant | Average:62.38; most accessible tissue: Zhenshan97 young leaf, score: 79.507 | N | N | N | N |
| vg0805653724 | G -> DEL | LOC_Os08g09780.2 | N | frameshift_variant | Average:62.38; most accessible tissue: Zhenshan97 young leaf, score: 79.507 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0805653724 | NA | 1.34E-06 | mr1038 | 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 |
| vg0805653724 | NA | 2.48E-07 | mr1389 | 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 |
| vg0805653724 | 1.20E-07 | NA | mr1807 | 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 |
| vg0805653724 | NA | 5.70E-06 | mr1125_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 |