Variant ID: vg0804593767 (JBrowse) | Variation Type: SNP |
Chromosome: chr08 | Position: 4593767 |
Reference Allele: G | Alternative Allele: C |
Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
ATCCAATTCCATCTCGATCATCTCCTCAGCTACTACTGCTTCATCGAATCGTCGAAGCATCAACAGCTATAGATCAAGTTCGAGAGGTTGATTCAGAGAG[G/C]
CATTGCAAATTAGCAATGGCGAGCGCGGCGGCGGCGGTGGCGGCGAAGGCGTGGTGGACGGCGGCGATGAGCGTGGGCGCGGTGGAGGGGCTCAAGGACC
GGTCCTTGAGCCCCTCCACCGCGCCCACGCTCATCGCCGCCGTCCACCACGCCTTCGCCGCCACCGCCGCCGCCGCGCTCGCCATTGCTAATTTGCAATG[C/G]
CTCTCTGAATCAACCTCTCGAACTTGATCTATAGCTGTTGATGCTTCGACGATTCGATGAAGCAGTAGTAGCTGAGGAGATGATCGAGATGGAATTGGAT
Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 91.60% | 8.40% | 0.04% | 0.00% | NA |
All Indica | 2759 | 95.70% | 4.20% | 0.07% | 0.00% | NA |
All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
Aus | 269 | 30.10% | 69.90% | 0.00% | 0.00% | NA |
Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica II | 465 | 93.80% | 6.20% | 0.00% | 0.00% | NA |
Indica III | 913 | 97.20% | 2.80% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 91.90% | 7.90% | 0.25% | 0.00% | NA |
Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 15.60% | 84.40% | 0.00% | 0.00% | NA |
Intermediate | 90 | 90.00% | 10.00% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0804593767 | G -> C | LOC_Os08g08090.1 | 5_prime_UTR_variant ; 16.0bp to feature; MODIFIER | silent_mutation | Average:76.203; most accessible tissue: Zhenshan97 flag leaf, score: 83.84 | N | N | N | N |
vg0804593767 | G -> C | LOC_Os08g08084.1 | upstream_gene_variant ; 887.0bp to feature; MODIFIER | silent_mutation | Average:76.203; most accessible tissue: Zhenshan97 flag leaf, score: 83.84 | N | N | N | N |
vg0804593767 | G -> C | LOC_Os08g08100.1 | upstream_gene_variant ; 2011.0bp to feature; MODIFIER | silent_mutation | Average:76.203; most accessible tissue: Zhenshan97 flag leaf, score: 83.84 | N | N | N | N |
vg0804593767 | G -> C | LOC_Os08g08080.1 | downstream_gene_variant ; 2528.0bp to feature; MODIFIER | silent_mutation | Average:76.203; most accessible tissue: Zhenshan97 flag leaf, score: 83.84 | N | N | N | N |
vg0804593767 | G -> C | LOC_Os08g08080.2 | downstream_gene_variant ; 2534.0bp to feature; MODIFIER | silent_mutation | Average:76.203; most accessible tissue: Zhenshan97 flag leaf, score: 83.84 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0804593767 | NA | 7.63E-09 | mr1166_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 |
vg0804593767 | NA | 1.59E-07 | mr1612_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 |
vg0804593767 | NA | 1.25E-07 | mr1808_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 |
vg0804593767 | NA | 5.13E-06 | mr1929_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 |
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