Variant ID: vg0723902655 (JBrowse) | Variation Type: SNP |
Chromosome: chr07 | Position: 23902655 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TGGATGCGGTTTCTCGGCGTGTTTTTTTTTTCTTTTTGTTCTGTTCAACCTGACGCTAGCAGAAGTTCAGAACTAGGAACTCGCCGTGGCAGACTTAGGG[C/T]
CTATTCACTTTAATGCCAAAAAAAACCTTACCAAATTTTAGCAACTTGCTAAAAATTTTGCAGGATTTCTTATATAGTTACCAAAATTTGGCAAGAAATT
AATTTCTTGCCAAATTTTGGTAACTATATAAGAAATCCTGCAAAATTTTTAGCAAGTTGCTAAAATTTGGTAAGGTTTTTTTTGGCATTAAAGTGAATAG[G/A]
CCCTAAGTCTGCCACGGCGAGTTCCTAGTTCTGAACTTCTGCTAGCGTCAGGTTGAACAGAACAAAAAGAAAAAAAAAACACGCCGAGAAACCGCATCCA
Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 96.50% | 2.90% | 0.57% | 0.00% | NA |
All Indica | 2759 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 89.60% | 8.60% | 1.79% | 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 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 92.80% | 4.30% | 2.87% | 0.00% | NA |
Tropical Japonica | 504 | 91.50% | 8.30% | 0.20% | 0.00% | NA |
Japonica Intermediate | 241 | 75.50% | 22.80% | 1.66% | 0.00% | NA |
VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
Intermediate | 90 | 95.60% | 4.40% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0723902655 | C -> T | LOC_Os07g39850.1 | upstream_gene_variant ; 3013.0bp to feature; MODIFIER | silent_mutation | Average:57.151; most accessible tissue: Minghui63 panicle, score: 75.788 | N | N | N | N |
vg0723902655 | C -> T | LOC_Os07g39860.1 | downstream_gene_variant ; 219.0bp to feature; MODIFIER | silent_mutation | Average:57.151; most accessible tissue: Minghui63 panicle, score: 75.788 | N | N | N | N |
vg0723902655 | C -> T | LOC_Os07g39870.1 | downstream_gene_variant ; 2265.0bp to feature; MODIFIER | silent_mutation | Average:57.151; most accessible tissue: Minghui63 panicle, score: 75.788 | N | N | N | N |
vg0723902655 | C -> T | LOC_Os07g39870.2 | downstream_gene_variant ; 2265.0bp to feature; MODIFIER | silent_mutation | Average:57.151; most accessible tissue: Minghui63 panicle, score: 75.788 | N | N | N | N |
vg0723902655 | C -> T | LOC_Os07g39870.3 | downstream_gene_variant ; 2265.0bp to feature; MODIFIER | silent_mutation | Average:57.151; most accessible tissue: Minghui63 panicle, score: 75.788 | N | N | N | N |
vg0723902655 | C -> T | LOC_Os07g39850-LOC_Os07g39860 | intergenic_region ; MODIFIER | silent_mutation | Average:57.151; most accessible tissue: Minghui63 panicle, score: 75.788 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0723902655 | 1.77E-06 | 1.98E-08 | mr1350_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 |