Variant ID: vg0400966446 (JBrowse) | Variation Type: SNP |
Chromosome: chr04 | Position: 966446 |
Reference Allele: A | Alternative Allele: C |
Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 80. )
TAAAAAAAAGTCAACAGCGTCATCTATTAAAAATATGAAGGTAGTAATAATTTTCCTATGTACCTAGCAGTTGCATTACTATCCACTTACTAGCCTACGC[A/C]
CCTAATTAGTTTATCTTATTATGTGTATAGGCGTATATATTGCTCATGCCCATATTATTTCTGTGTGGGACCTGTGTTTTACGGCTAAATGTAAAAAAAA
TTTTTTTTACATTTAGCCGTAAAACACAGGTCCCACACAGAAATAATATGGGCATGAGCAATATATACGCCTATACACATAATAAGATAAACTAATTAGG[T/G]
GCGTAGGCTAGTAAGTGGATAGTAATGCAACTGCTAGGTACATAGGAAAATTATTACTACCTTCATATTTTTAATAGATGACGCTGTTGACTTTTTTTTA
Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 54.60% | 44.70% | 0.25% | 0.40% | NA |
All Indica | 2759 | 62.70% | 36.30% | 0.29% | 0.69% | NA |
All Japonica | 1512 | 39.00% | 60.90% | 0.07% | 0.00% | NA |
Aus | 269 | 75.80% | 23.80% | 0.37% | 0.00% | NA |
Indica I | 595 | 79.20% | 20.80% | 0.00% | 0.00% | NA |
Indica II | 465 | 54.40% | 44.70% | 0.00% | 0.86% | NA |
Indica III | 913 | 66.00% | 32.00% | 0.66% | 1.31% | NA |
Indica Intermediate | 786 | 51.30% | 48.10% | 0.25% | 0.38% | NA |
Temperate Japonica | 767 | 62.30% | 37.70% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 15.10% | 84.90% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 14.90% | 84.60% | 0.41% | 0.00% | NA |
VI/Aromatic | 96 | 17.70% | 80.20% | 2.08% | 0.00% | NA |
Intermediate | 90 | 45.60% | 54.40% | 0.00% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0400966446 | A -> C | LOC_Os04g02570.1 | downstream_gene_variant ; 697.0bp to feature; MODIFIER | silent_mutation | Average:43.678; most accessible tissue: Callus, score: 79.25 | N | N | N | N |
vg0400966446 | A -> C | LOC_Os04g02580.1 | downstream_gene_variant ; 1521.0bp to feature; MODIFIER | silent_mutation | Average:43.678; most accessible tissue: Callus, score: 79.25 | N | N | N | N |
vg0400966446 | A -> C | LOC_Os04g02560-LOC_Os04g02570 | intergenic_region ; MODIFIER | silent_mutation | Average:43.678; most accessible tissue: Callus, score: 79.25 | N | N | N | N |
vg0400966446 | A -> DEL | N | N | silent_mutation | Average:43.678; most accessible tissue: Callus, score: 79.25 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0400966446 | NA | 9.92E-06 | mr1182 | 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 |
vg0400966446 | NA | 2.61E-06 | mr1650 | 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 |
vg0400966446 | 7.18E-06 | 7.06E-07 | mr1242_2 | 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 |
vg0400966446 | NA | 9.91E-06 | mr1631_2 | 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 |
vg0400966446 | NA | 6.77E-06 | mr1835_2 | 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 |
vg0400966446 | 2.64E-06 | 3.50E-09 | mr1904_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 |