Variant ID: vg1127840259 (JBrowse) | Variation Type: SNP |
Chromosome: chr11 | Position: 27840259 |
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: 46. )
AACGAAGAGAGTATGTAGCTACATTTTAAGGCTGAGGAAGCGTTTTTAACATTCCCACTCGAGAAACTCATGTTAGCTAAACATTAGAAAACCCCATGCT[T/C]
TATGGTCAAAGTTGCATAAAACCCAAAATATCATCACCAGTGTCACATTACTCTAGGTTTTATGGTTCTAAAGTTTTACAATACCCCACCCTATATGTGT
ACACATATAGGGTGGGGTATTGTAAAACTTTAGAACCATAAAACCTAGAGTAATGTGACACTGGTGATGATATTTTGGGTTTTATGCAACTTTGACCATA[A/G]
AGCATGGGGTTTTCTAATGTTTAGCTAACATGAGTTTCTCGAGTGGGAATGTTAAAAACGCTTCCTCAGCCTTAAAATGTAGCTACATACTCTCTTCGTT
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 | 54.30% | 25.30% | 17.18% | 3.24% | NA |
All Indica | 2759 | 49.10% | 34.00% | 13.56% | 3.37% | NA |
All Japonica | 1512 | 63.90% | 9.90% | 22.75% | 3.44% | NA |
Aus | 269 | 59.90% | 23.40% | 14.50% | 2.23% | NA |
Indica I | 595 | 32.40% | 38.70% | 22.18% | 6.72% | NA |
Indica II | 465 | 52.70% | 31.80% | 14.84% | 0.65% | NA |
Indica III | 913 | 58.70% | 31.70% | 7.67% | 1.97% | NA |
Indica Intermediate | 786 | 48.30% | 34.50% | 13.10% | 4.07% | NA |
Temperate Japonica | 767 | 50.30% | 14.90% | 30.77% | 4.04% | NA |
Tropical Japonica | 504 | 83.50% | 3.40% | 11.11% | 1.98% | NA |
Japonica Intermediate | 241 | 66.00% | 7.90% | 21.58% | 4.56% | NA |
VI/Aromatic | 96 | 27.10% | 37.50% | 34.38% | 1.04% | NA |
Intermediate | 90 | 64.40% | 10.00% | 24.44% | 1.11% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg1127840259 | T -> DEL | N | N | silent_mutation | Average:35.869; most accessible tissue: Minghui63 panicle, score: 66.554 | N | N | N | N |
vg1127840259 | T -> C | LOC_Os11g46000.1 | upstream_gene_variant ; 1254.0bp to feature; MODIFIER | silent_mutation | Average:35.869; most accessible tissue: Minghui63 panicle, score: 66.554 | N | N | N | N |
vg1127840259 | T -> C | LOC_Os11g46000.2 | upstream_gene_variant ; 1254.0bp to feature; MODIFIER | silent_mutation | Average:35.869; most accessible tissue: Minghui63 panicle, score: 66.554 | N | N | N | N |
vg1127840259 | T -> C | LOC_Os11g46000.3 | upstream_gene_variant ; 1785.0bp to feature; MODIFIER | silent_mutation | Average:35.869; most accessible tissue: Minghui63 panicle, score: 66.554 | N | N | N | N |
vg1127840259 | T -> C | LOC_Os11g45990-LOC_Os11g46000 | intergenic_region ; MODIFIER | silent_mutation | Average:35.869; most accessible tissue: Minghui63 panicle, score: 66.554 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1127840259 | 1.47E-06 | 2.00E-06 | mr1337 | 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 |
vg1127840259 | 5.48E-06 | 5.46E-06 | mr1429 | 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 |