Search for Variation information by Variation ID:
Detailed information for vg0404609499:
| Variant ID: vg0404609499 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 4609499 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 250. )
Flanking Sequence (100 bp) in Reference Genome:
CCCACAGGTTTACACCTATATGGTCGCTCTCTCACCTCCCAAGTCCCGTTAGCGATAATGGAATCCATTTCACTACGGATAGCCTCCTTCCAGTAGTCTG[C/T]
ATCAGAAGATGCATATGCTTCTGAAATTGACTTAGGAGTGTCATCCATGAGGTACACAGTGAAATCATCACCAAAAGACTTAGCCGTCCTTTGTCTCTTA
Reverse complement sequence
TAAGAGACAAAGGACGGCTAAGTCTTTTGGTGATGATTTCACTGTGTACCTCATGGATGACACTCCTAAGTCAATTTCAGAAGCATATGCATCTTCTGAT[G/A]
CAGACTACTGGAAGGAGGCTATCCGTAGTGAAATGGATTCCATTATCGCTAACGGGACTTGGGAGGTGAGAGAGCGACCATATAGGTGTAAACCTGTGGG
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 84.10% | 13.90% | 1.25% | 0.76% | NA |
| All Indica | 2759 | 78.50% | 20.30% | 0.43% | 0.76% | NA |
| All Japonica | 1512 | 95.20% | 4.80% | 0.07% | 0.00% | NA |
| Aus | 269 | 72.10% | 6.30% | 16.36% | 5.20% | NA |
| Indica I | 595 | 93.80% | 6.10% | 0.17% | 0.00% | NA |
| Indica II | 465 | 83.40% | 12.90% | 1.08% | 2.58% | NA |
| Indica III | 913 | 66.00% | 33.10% | 0.33% | 0.55% | NA |
| Indica Intermediate | 786 | 78.40% | 20.70% | 0.38% | 0.51% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 86.50% | 13.30% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 90.00% | 7.80% | 2.22% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0404609499 | C -> DEL | LOC_Os04g08520.1 | N | frameshift_variant | Average:19.061; most accessible tissue: Minghui63 young leaf, score: 33.985 | N | N | N | N |
| vg0404609499 | C -> T | LOC_Os04g08520.1 | missense_variant ; p.Ala351Thr; MODERATE | nonsynonymous_codon ; A351T | Average:19.061; most accessible tissue: Minghui63 young leaf, score: 33.985 | possibly damaging  |
1.67 |
DELETERIOUS | 0.02 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0404609499 | NA | 4.42E-06 | mr1798 | 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 |
| vg0404609499 | 3.37E-06 | NA | mr1798_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 |
| vg0404609499 | 9.58E-08 | 2.06E-10 | mr1798_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 |