Search for Variation information by Variation ID:
Detailed information for vg0624653619:
| Variant ID: vg0624653619 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 24653619 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 107. )
Flanking Sequence (100 bp) in Reference Genome:
AGACCCTCCTCCTCTGTTCACCACTCACTACCTTTTCAGCTCCTACATCGCACCACCCTAGACTACTCCCACCTTCGCGTCTTTGGCTGTCTTTGTTACC[C/T]
AAACTTGAGTGCCACGACTCCACATAAGCTTGCCCCTCGCTCGACAACTTGCTTTTTTCTTGGGTACCCGGCCTCCCACAAGGGATACCGATGTCTGGAT
Reverse complement sequence
ATCCAGACATCGGTATCCCTTGTGGGAGGCCGGGTACCCAAGAAAAAAGCAAGTTGTCGAGCGAGGGGCAAGCTTATGTGGAGTCGTGGCACTCAAGTTT[G/A]
GGTAACAAAGACAGCCAAAGACGCGAAGGTGGGAGTAGTCTAGGGTGGTGCGATGTAGGAGCTGAAAAGGTAGTGAGTGGTGAACAGAGGAGGAGGGTCT
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 | 34.50% | 10.70% | 8.80% | 45.98% | NA |
| All Indica | 2759 | 5.10% | 15.20% | 11.49% | 68.21% | NA |
| All Japonica | 1512 | 89.30% | 0.00% | 2.31% | 8.40% | NA |
| Aus | 269 | 5.90% | 32.70% | 19.70% | 41.64% | NA |
| Indica I | 595 | 3.50% | 1.30% | 3.70% | 91.43% | NA |
| Indica II | 465 | 3.70% | 1.90% | 6.24% | 88.17% | NA |
| Indica III | 913 | 3.80% | 36.00% | 19.50% | 40.64% | NA |
| Indica Intermediate | 786 | 8.70% | 9.30% | 11.20% | 70.87% | NA |
| Temperate Japonica | 767 | 97.80% | 0.00% | 0.13% | 2.09% | NA |
| Tropical Japonica | 504 | 72.60% | 0.00% | 6.35% | 21.03% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.00% | 0.83% | 2.07% | NA |
| VI/Aromatic | 96 | 84.40% | 0.00% | 4.17% | 11.46% | NA |
| Intermediate | 90 | 45.60% | 1.10% | 7.78% | 45.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0624653619 | C -> T | LOC_Os06g41200.1 | missense_variant ; p.Pro66Leu; MODERATE | nonsynonymous_codon ; P66L | Average:5.409; most accessible tissue: Callus, score: 14.826 | probably damaging  |
2.37 |
DELETERIOUS | 0.00 |
| vg0624653619 | C -> DEL | LOC_Os06g41200.1 | N | frameshift_variant | Average:5.409; most accessible tissue: Callus, score: 14.826 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0624653619 | 3.63E-06 | 3.63E-06 | mr1348 | 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 |
| vg0624653619 | NA | 8.72E-06 | mr1508 | 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 |
| vg0624653619 | NA | 6.47E-07 | mr1812 | 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 |