Variant ID: vg0724533303 (JBrowse) | Variation Type: SNP |
Chromosome: chr07 | Position: 24533303 |
Reference Allele: T | Alternative Allele: C |
Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 236. )
CAATTTCATATTTTTTGAGTGTACTGTAGCAAATTTTGCCTTTTATTTTTGATAGGCATATTTCAATCCAACAACCTATCCTCTTAATAACTTTCTCGGA[T/C]
TCAATGCGTCACTCTCCATTCTTCCACACAAGATTGGCTATATGGGCATCGAGAAATGTAATAATTAATTAATCGTTTGTTTACGAGGAATAACTAGTAG
CTACTAGTTATTCCTCGTAAACAAACGATTAATTAATTATTACATTTCTCGATGCCCATATAGCCAATCTTGTGTGGAAGAATGGAGAGTGACGCATTGA[A/G]
TCCGAGAAAGTTATTAAGAGGATAGGTTGTTGGATTGAAATATGCCTATCAAAAATAAAAGGCAAAATTTGCTACAGTACACTCAAAAAATATGAAATTG
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 | 96.00% | 3.60% | 0.40% | 0.00% | NA |
All Indica | 2759 | 98.70% | 1.30% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 90.50% | 8.30% | 1.19% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica II | 465 | 94.20% | 5.80% | 0.00% | 0.00% | NA |
Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 99.50% | 0.30% | 0.26% | 0.00% | NA |
Tropical Japonica | 504 | 76.00% | 21.00% | 2.98% | 0.00% | NA |
Japonica Intermediate | 241 | 92.50% | 7.10% | 0.41% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 87.80% | 11.10% | 1.11% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0724533303 | T -> C | LOC_Os07g41000.1 | upstream_gene_variant ; 957.0bp to feature; MODIFIER | silent_mutation | Average:22.088; most accessible tissue: Callus, score: 48.034 | N | N | N | N |
vg0724533303 | T -> C | LOC_Os07g41014.1 | downstream_gene_variant ; 1071.0bp to feature; MODIFIER | silent_mutation | Average:22.088; most accessible tissue: Callus, score: 48.034 | N | N | N | N |
vg0724533303 | T -> C | LOC_Os07g41000-LOC_Os07g41014 | intergenic_region ; MODIFIER | silent_mutation | Average:22.088; most accessible tissue: Callus, score: 48.034 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0724533303 | NA | 4.50E-13 | Grain_width | Jap_All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
vg0724533303 | 1.28E-06 | NA | mr1301 | 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 |
vg0724533303 | NA | 2.11E-06 | mr1583 | 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 |
vg0724533303 | 2.74E-08 | NA | mr1301_2 | 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 |
vg0724533303 | 4.00E-06 | NA | mr1410_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 |