Variant ID: vg0135250174 (JBrowse) | Variation Type: SNP |
Chromosome: chr01 | Position: 35250174 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.73, T: 0.28, others allele: 0.00, population size: 94. )
GAAAACGGAGCGGATACGGATGGATAATGCTCATACCATATTCGTTTTCATATTTTTTTACCGGATACGAAAACGAATACGGATAGCTCGAATACGGAAA[C/T]
AAATACGGATTATCTCGAATACGAATAAGAATCGAATATGATCGGACATGAATACGGAAACAATTTTTTCTCAGAACACGAAAACCAACTCAACTTCTAA
TTAGAAGTTGAGTTGGTTTTCGTGTTCTGAGAAAAAATTGTTTCCGTATTCATGTCCGATCATATTCGATTCTTATTCGTATTCGAGATAATCCGTATTT[G/A]
TTTCCGTATTCGAGCTATCCGTATTCGTTTTCGTATCCGGTAAAAAAATATGAAAACGAATATGGTATGAGCATTATCCATCCGTATCCGCTCCGTTTTC
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 | 80.90% | 15.50% | 2.58% | 0.95% | NA |
All Indica | 2759 | 96.30% | 1.50% | 0.58% | 1.59% | NA |
All Japonica | 1512 | 53.40% | 41.10% | 5.56% | 0.00% | NA |
Aus | 269 | 99.60% | 0.00% | 0.37% | 0.00% | NA |
Indica I | 595 | 96.10% | 3.70% | 0.17% | 0.00% | NA |
Indica II | 465 | 92.00% | 0.00% | 1.29% | 6.67% | NA |
Indica III | 913 | 99.70% | 0.10% | 0.22% | 0.00% | NA |
Indica Intermediate | 786 | 95.20% | 2.30% | 0.89% | 1.65% | NA |
Temperate Japonica | 767 | 66.60% | 28.30% | 5.08% | 0.00% | NA |
Tropical Japonica | 504 | 35.70% | 57.30% | 6.94% | 0.00% | NA |
Japonica Intermediate | 241 | 48.10% | 47.70% | 4.15% | 0.00% | NA |
VI/Aromatic | 96 | 29.20% | 50.00% | 20.83% | 0.00% | NA |
Intermediate | 90 | 71.10% | 26.70% | 1.11% | 1.11% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0135250174 | C -> T | LOC_Os01g60930.1 | downstream_gene_variant ; 3366.0bp to feature; MODIFIER | silent_mutation | Average:41.402; most accessible tissue: Zhenshan97 panicle, score: 68.538 | N | N | N | N |
vg0135250174 | C -> T | LOC_Os01g60940.1 | downstream_gene_variant ; 1248.0bp to feature; MODIFIER | silent_mutation | Average:41.402; most accessible tissue: Zhenshan97 panicle, score: 68.538 | N | N | N | N |
vg0135250174 | C -> T | LOC_Os01g60940-LOC_Os01g60960 | intergenic_region ; MODIFIER | silent_mutation | Average:41.402; most accessible tissue: Zhenshan97 panicle, score: 68.538 | N | N | N | N |
vg0135250174 | C -> DEL | N | N | silent_mutation | Average:41.402; most accessible tissue: Zhenshan97 panicle, score: 68.538 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0135250174 | 1.50E-06 | NA | mr1712 | 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 |
vg0135250174 | NA | 1.01E-06 | mr1712 | 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 |
vg0135250174 | NA | 6.73E-06 | mr1826_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 |