Variant ID: vg0103148298 (JBrowse) | Variation Type: SNP |
Chromosome: chr01 | Position: 3148298 |
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. )
TCTCCGACACATCCCCCCATTGCTCGATGGTGCTTATGAGGGGTTGGAACTTGTCGGGAACGGAATGCAAGAGCTTCTCCACCACCGTGGTCTCCTCCAC[T/C]
TTCGTGCCGAGAGAGCGAATCTCGTTCACGATCGTGGTAACCTTTAAAGCAAAATCATTAATTTTCTCAGAATTACTCATGTACATACCATCAAGCTCCC
GGGAGCTTGATGGTATGTACATGAGTAATTCTGAGAAAATTAATGATTTTGCTTTAAAGGTTACCACGATCGTGAACGAGATTCGCTCTCTCGGCACGAA[A/G]
GTGGAGGAGACCACGGTGGTGGAGAAGCTCTTGCATTCCGTTCCCGACAAGTTCCAACCCCTCATAAGCACCATCGAGCAATGGGGGGATGTGTCGGAGA
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 | 59.70% | 12.20% | 3.11% | 24.97% | NA |
All Indica | 2759 | 75.10% | 2.00% | 2.25% | 20.66% | NA |
All Japonica | 1512 | 22.00% | 33.90% | 5.36% | 38.76% | NA |
Aus | 269 | 96.70% | 0.00% | 0.00% | 3.35% | NA |
Indica I | 595 | 94.80% | 0.00% | 0.34% | 4.87% | NA |
Indica II | 465 | 77.60% | 2.20% | 1.08% | 19.14% | NA |
Indica III | 913 | 66.30% | 2.20% | 3.72% | 27.82% | NA |
Indica Intermediate | 786 | 69.10% | 3.10% | 2.67% | 25.19% | NA |
Temperate Japonica | 767 | 29.20% | 13.30% | 1.56% | 55.93% | NA |
Tropical Japonica | 504 | 11.50% | 58.90% | 9.52% | 20.04% | NA |
Japonica Intermediate | 241 | 21.20% | 46.90% | 8.71% | 23.24% | NA |
VI/Aromatic | 96 | 94.80% | 1.00% | 0.00% | 4.17% | NA |
Intermediate | 90 | 73.30% | 10.00% | 4.44% | 12.22% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0103148298 | T -> DEL | LOC_Os01g06680.1 | N | frameshift_variant | Average:57.3; most accessible tissue: Callus, score: 95.813 | N | N | N | N |
vg0103148298 | T -> C | LOC_Os01g06680.1 | synonymous_variant ; p.Lys654Lys; LOW | synonymous_codon | Average:57.3; most accessible tissue: Callus, score: 95.813 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0103148298 | NA | 8.31E-07 | mr1245 | 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 |
vg0103148298 | NA | 1.89E-06 | mr1392 | 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 |
vg0103148298 | 9.02E-07 | NA | mr1403 | 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 |
vg0103148298 | 5.61E-06 | NA | mr1403 | 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 |
vg0103148298 | NA | 7.94E-07 | mr1445 | 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 |
vg0103148298 | NA | 1.16E-11 | mr1636 | 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 |
vg0103148298 | NA | 3.78E-11 | mr1751 | 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 |
vg0103148298 | NA | 2.96E-08 | mr1779 | 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 |