Search for Variation information by Variation ID:
Detailed information for vg1000740409:
| Variant ID: vg1000740409 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 740409 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.84, T: 0.16, others allele: 0.00, population size: 93. )
Flanking Sequence (100 bp) in Reference Genome:
TCAGACCACTTCATCTTGGGTGCAGCCCCCTGCCATGTCGAACAAACCTCACGTTCCACTTTTTTGTATTCTCGCTTTGAAGAGTACACTATGGAGCCTC[T/C]
GAAGATGTGCGAGACATGAAGATCGGAATCTGGGTATGTGAAGTCCGAATCCTGAGTGGTTGCCTCAGTGGCCTTCTCGACTACACGTACTTGCTTGCCC
Reverse complement sequence
GGGCAAGCAAGTACGTGTAGTCGAGAAGGCCACTGAGGCAACCACTCAGGATTCGGACTTCACATACCCAGATTCCGATCTTCATGTCTCGCACATCTTC[A/G]
GAGGCTCCATAGTGTACTCTTCAAAGCGAGAATACAAAAAAGTGGAACGTGAGGTTTGTTCGACATGGCAGGGGGCTGCACCCAAGATGAAGTGGTCTGA
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 | 42.10% | 16.60% | 0.87% | 40.48% | NA |
| All Indica | 2759 | 53.00% | 0.80% | 1.16% | 44.98% | NA |
| All Japonica | 1512 | 8.90% | 48.60% | 0.46% | 42.00% | NA |
| Aus | 269 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 63.00% | 1.00% | 1.51% | 34.45% | NA |
| Indica II | 465 | 25.40% | 0.90% | 1.51% | 72.26% | NA |
| Indica III | 913 | 55.00% | 0.20% | 0.44% | 44.36% | NA |
| Indica Intermediate | 786 | 59.50% | 1.40% | 1.53% | 37.53% | NA |
| Temperate Japonica | 767 | 10.40% | 78.00% | 0.65% | 10.95% | NA |
| Tropical Japonica | 504 | 3.80% | 5.80% | 0.40% | 90.08% | NA |
| Japonica Intermediate | 241 | 14.90% | 44.80% | 0.00% | 40.25% | NA |
| VI/Aromatic | 96 | 93.80% | 6.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 36.70% | 20.00% | 2.22% | 41.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1000740409 | T -> C | LOC_Os10g02170.1 | missense_variant ; p.Arg305Gly; MODERATE | nonsynonymous_codon ; R305E | Average:22.455; most accessible tissue: Zhenshan97 flag leaf, score: 66.327 | benign  |
-0.427 |
TOLERATED | 0.22 |
| vg1000740409 | T -> C | LOC_Os10g02170.1 | missense_variant ; p.Arg305Gly; MODERATE | nonsynonymous_codon ; R305G | Average:22.455; most accessible tissue: Zhenshan97 flag leaf, score: 66.327 | benign |
-0.339 |
TOLERATED | 1.00 |
| vg1000740409 | T -> DEL | LOC_Os10g02170.1 | N | frameshift_variant | Average:22.455; most accessible tissue: Zhenshan97 flag leaf, score: 66.327 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1000740409 | 6.38E-06 | NA | mr1310 | 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 |
| vg1000740409 | NA | 1.68E-08 | mr1498 | 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 |
| vg1000740409 | 1.78E-06 | NA | mr1926 | 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 |
| vg1000740409 | 3.91E-07 | NA | mr1926 | 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 |
| vg1000740409 | 4.20E-10 | NA | mr1310_2 | 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 |
| vg1000740409 | 3.80E-09 | NA | mr1310_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 |
| vg1000740409 | 2.78E-08 | NA | mr1959_2 | 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 |