Variant ID: vg0431033243 (JBrowse) | Variation Type: SNP |
Chromosome: chr04 | Position: 31033243 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TATTTTTGAGAATTACACAGTACAACGCAGACACTTACAATGTACGCACACTCACCCCTACGAACGCACGCATGTAAACTCTACCCCTATGAGCATATTC[G/A]
AAGACTGGGCCGGCAAATCCTAGAGATTGACGAAGTCACCACAGGCGTCTCACTGTCGACGGGTACGTCGCCTAGACTAGGTGCGAACTACTGTCCAGAG
CTCTGGACAGTAGTTCGCACCTAGTCTAGGCGACGTACCCGTCGACAGTGAGACGCCTGTGGTGACTTCGTCAATCTCTAGGATTTGCCGGCCCAGTCTT[C/T]
GAATATGCTCATAGGGGTAGAGTTTACATGCGTGCGTTCGTAGGGGTGAGTGTGCGTACATTGTAAGTGTCTGCGTTGTACTGTGTAATTCTCAAAAATA
Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 97.20% | 2.80% | 0.06% | 0.00% | NA |
All Indica | 2759 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 91.70% | 8.10% | 0.20% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 83.80% | 15.80% | 0.39% | 0.00% | NA |
Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 100.00% | 0.00% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0431033243 | G -> A | LOC_Os04g52240.1 | upstream_gene_variant ; 1803.0bp to feature; MODIFIER | silent_mutation | Average:49.633; most accessible tissue: Zhenshan97 panicle, score: 69.946 | N | N | N | N |
vg0431033243 | G -> A | LOC_Os04g52230.1 | downstream_gene_variant ; 1995.0bp to feature; MODIFIER | silent_mutation | Average:49.633; most accessible tissue: Zhenshan97 panicle, score: 69.946 | N | N | N | N |
vg0431033243 | G -> A | LOC_Os04g52230-LOC_Os04g52240 | intergenic_region ; MODIFIER | silent_mutation | Average:49.633; most accessible tissue: Zhenshan97 panicle, score: 69.946 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0431033243 | NA | 3.94E-07 | mr1062_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 |
vg0431033243 | 2.55E-06 | 2.55E-06 | mr1445_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 |