Variant ID: vg0401805850 (JBrowse) | Variation Type: SNP |
Chromosome: chr04 | Position: 1805850 |
Reference Allele: C | Alternative Allele: A,T |
Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CTAATCATATAGTCGGGGGCTACACCTAATTAGGTGCATCTATTCGATGCACCATGTTTTTTATTTTTCGCCCTTTACAGTCTTCGTCTTCGCTACTCGG[C/A,T]
AGGCCTTAGCAGGAAAAATTAAAGCACTCGGATTATTATTTTTTGAGAGAGCTATGTTGTCGACTGCAAAGGTCTCGGGGGCTACTGTGGAGATTATGGA
TCCATAATCTCCACAGTAGCCCCCGAGACCTTTGCAGTCGACAACATAGCTCTCTCAAAAAATAATAATCCGAGTGCTTTAATTTTTCCTGCTAAGGCCT[G/T,A]
CCGAGTAGCGAAGACGAAGACTGTAAAGGGCGAAAAATAAAAAACATGGTGCATCGAATAGATGCACCTAATTAGGTGTAGCCCCCGACTATATGATTAG
Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 89.20% | 1.00% | 2.01% | 7.66% | T: 0.08% |
All Indica | 2759 | 83.70% | 1.30% | 2.79% | 12.11% | T: 0.11% |
All Japonica | 1512 | 98.50% | 0.10% | 0.26% | 1.19% | NA |
Aus | 269 | 92.20% | 3.00% | 4.46% | 0.37% | NA |
Indica I | 595 | 85.40% | 1.00% | 2.86% | 10.76% | NA |
Indica II | 465 | 79.80% | 0.20% | 0.86% | 18.92% | T: 0.22% |
Indica III | 913 | 81.90% | 2.50% | 4.16% | 11.28% | T: 0.11% |
Indica Intermediate | 786 | 86.80% | 0.80% | 2.29% | 10.05% | T: 0.13% |
Temperate Japonica | 767 | 99.70% | 0.00% | 0.00% | 0.26% | NA |
Tropical Japonica | 504 | 96.60% | 0.00% | 0.40% | 2.98% | NA |
Japonica Intermediate | 241 | 98.30% | 0.40% | 0.83% | 0.41% | NA |
VI/Aromatic | 96 | 95.80% | 2.10% | 2.08% | 0.00% | NA |
Intermediate | 90 | 86.70% | 2.20% | 0.00% | 10.00% | T: 1.11% |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0401805850 | C -> DEL | N | N | silent_mutation | Average:25.553; most accessible tissue: Minghui63 young leaf, score: 44.63 | N | N | N | N |
vg0401805850 | C -> A | LOC_Os04g03950.1 | upstream_gene_variant ; 929.0bp to feature; MODIFIER | silent_mutation | Average:25.553; most accessible tissue: Minghui63 young leaf, score: 44.63 | N | N | N | N |
vg0401805850 | C -> A | LOC_Os04g03970.1 | upstream_gene_variant ; 2619.0bp to feature; MODIFIER | silent_mutation | Average:25.553; most accessible tissue: Minghui63 young leaf, score: 44.63 | N | N | N | N |
vg0401805850 | C -> A | LOC_Os04g03960.1 | downstream_gene_variant ; 659.0bp to feature; MODIFIER | silent_mutation | Average:25.553; most accessible tissue: Minghui63 young leaf, score: 44.63 | N | N | N | N |
vg0401805850 | C -> A | LOC_Os04g03950-LOC_Os04g03960 | intergenic_region ; MODIFIER | silent_mutation | Average:25.553; most accessible tissue: Minghui63 young leaf, score: 44.63 | N | N | N | N |
vg0401805850 | C -> T | LOC_Os04g03950.1 | upstream_gene_variant ; 929.0bp to feature; MODIFIER | silent_mutation | Average:25.553; most accessible tissue: Minghui63 young leaf, score: 44.63 | N | N | N | N |
vg0401805850 | C -> T | LOC_Os04g03970.1 | upstream_gene_variant ; 2619.0bp to feature; MODIFIER | silent_mutation | Average:25.553; most accessible tissue: Minghui63 young leaf, score: 44.63 | N | N | N | N |
vg0401805850 | C -> T | LOC_Os04g03960.1 | downstream_gene_variant ; 659.0bp to feature; MODIFIER | silent_mutation | Average:25.553; most accessible tissue: Minghui63 young leaf, score: 44.63 | N | N | N | N |
vg0401805850 | C -> T | LOC_Os04g03950-LOC_Os04g03960 | intergenic_region ; MODIFIER | silent_mutation | Average:25.553; most accessible tissue: Minghui63 young leaf, score: 44.63 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0401805850 | 2.08E-06 | NA | mr1075_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 |