Variant ID: vg0718376392 (JBrowse) | Variation Type: SNP |
Chromosome: chr07 | Position: 18376392 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TCATCCGTGACGGGTTTAAGTTAAAGCCCGTCACCGATGAGTATTTCCTCCCAAAAAATAAATTCTGTTTTTTCGCTAGCCTCAGGCCTTTACTAGCCAT[G/A]
CCCGTTGTAAAATGAAGAAACAAATATATTTCACAATATCCCAGCATCCCCAATCATATACAATCATTCACATACACATATGCTATTCACATATTTCATA
TATGAAATATGTGAATAGCATATGTGTATGTGAATGATTGTATATGATTGGGGATGCTGGGATATTGTGAAATATATTTGTTTCTTCATTTTACAACGGG[C/T]
ATGGCTAGTAAAGGCCTGAGGCTAGCGAAAAAACAGAATTTATTTTTTGGGAGGAAATACTCATCGGTGACGGGCTTTAACTTAAACCCGTCACGGATGA
Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 26.50% | 18.60% | 22.26% | 32.63% | NA |
All Indica | 2759 | 24.20% | 11.60% | 31.93% | 32.22% | NA |
All Japonica | 1512 | 30.30% | 33.80% | 5.36% | 30.56% | NA |
Aus | 269 | 3.30% | 10.40% | 27.51% | 58.74% | NA |
Indica I | 595 | 18.00% | 6.40% | 11.60% | 64.03% | NA |
Indica II | 465 | 10.80% | 10.80% | 42.58% | 35.91% | NA |
Indica III | 913 | 29.50% | 15.30% | 38.12% | 17.09% | NA |
Indica Intermediate | 786 | 30.90% | 11.70% | 33.84% | 23.54% | NA |
Temperate Japonica | 767 | 22.00% | 50.20% | 8.21% | 19.56% | NA |
Tropical Japonica | 504 | 37.90% | 11.30% | 2.58% | 48.21% | NA |
Japonica Intermediate | 241 | 40.70% | 28.60% | 2.07% | 28.63% | NA |
VI/Aromatic | 96 | 88.50% | 0.00% | 2.08% | 9.38% | NA |
Intermediate | 90 | 35.60% | 22.20% | 15.56% | 26.67% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0718376392 | G -> DEL | N | N | silent_mutation | Average:15.784; most accessible tissue: Callus, score: 39.772 | N | N | N | N |
vg0718376392 | G -> A | LOC_Os07g31040.1 | upstream_gene_variant ; 3862.0bp to feature; MODIFIER | silent_mutation | Average:15.784; most accessible tissue: Callus, score: 39.772 | N | N | N | N |
vg0718376392 | G -> A | LOC_Os07g31020.1 | downstream_gene_variant ; 3652.0bp to feature; MODIFIER | silent_mutation | Average:15.784; most accessible tissue: Callus, score: 39.772 | N | N | N | N |
vg0718376392 | G -> A | LOC_Os07g31030.1 | downstream_gene_variant ; 665.0bp to feature; MODIFIER | silent_mutation | Average:15.784; most accessible tissue: Callus, score: 39.772 | N | N | N | N |
vg0718376392 | G -> A | LOC_Os07g31030-LOC_Os07g31040 | intergenic_region ; MODIFIER | silent_mutation | Average:15.784; most accessible tissue: Callus, score: 39.772 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0718376392 | NA | 5.47E-06 | mr1910 | 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 |
vg0718376392 | NA | 2.51E-11 | mr1399_2 | 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 |
vg0718376392 | NA | 3.76E-07 | mr1754_2 | 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 |