Variant ID: vg0421388213 (JBrowse) | Variation Type: SNP |
Chromosome: chr04 | Position: 21388213 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.03, others allele: 0.00, population size: 186. )
TTTCACTCGTTTAAATCAGGTGTTGTTTCACCTTATATAAAAACAATGTTTCAGCAAATAGTGAAAGAATGTTTCAGTTCACTACAACATTAGATTTATA[C/T]
ATAGTGAAACATTATGATTGCACTAGGTGAAACTGTTTGATGGTATTTTGGTGATTATACATGTACACAAGACTTACTCATGATGGACAAAGCAAACAAG
CTTGTTTGCTTTGTCCATCATGAGTAAGTCTTGTGTACATGTATAATCACCAAAATACCATCAAACAGTTTCACCTAGTGCAATCATAATGTTTCACTAT[G/A]
TATAAATCTAATGTTGTAGTGAACTGAAACATTCTTTCACTATTTGCTGAAACATTGTTTTTATATAAGGTGAAACAACACCTGATTTAAACGAGTGAAA
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 | 74.00% | 7.00% | 2.03% | 16.93% | NA |
All Indica | 2759 | 61.70% | 6.90% | 3.30% | 28.09% | NA |
All Japonica | 1512 | 94.30% | 5.60% | 0.07% | 0.07% | NA |
Aus | 269 | 90.70% | 4.50% | 0.37% | 4.46% | NA |
Indica I | 595 | 76.60% | 7.10% | 1.51% | 14.79% | NA |
Indica II | 465 | 77.40% | 0.90% | 2.58% | 19.14% | NA |
Indica III | 913 | 44.60% | 10.40% | 3.07% | 41.95% | NA |
Indica Intermediate | 786 | 61.10% | 6.20% | 5.34% | 27.35% | NA |
Temperate Japonica | 767 | 93.40% | 6.50% | 0.13% | 0.00% | NA |
Tropical Japonica | 504 | 93.10% | 6.70% | 0.00% | 0.20% | NA |
Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 54.20% | 40.60% | 1.04% | 4.17% | NA |
Intermediate | 90 | 81.10% | 7.80% | 2.22% | 8.89% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0421388213 | C -> DEL | N | N | silent_mutation | Average:51.268; most accessible tissue: Callus, score: 77.392 | N | N | N | N |
vg0421388213 | C -> T | LOC_Os04g35200.1 | upstream_gene_variant ; 621.0bp to feature; MODIFIER | silent_mutation | Average:51.268; most accessible tissue: Callus, score: 77.392 | N | N | N | N |
vg0421388213 | C -> T | LOC_Os04g35190.1 | downstream_gene_variant ; 2861.0bp to feature; MODIFIER | silent_mutation | Average:51.268; most accessible tissue: Callus, score: 77.392 | N | N | N | N |
vg0421388213 | C -> T | LOC_Os04g35200-LOC_Os04g35210 | intergenic_region ; MODIFIER | silent_mutation | Average:51.268; most accessible tissue: Callus, score: 77.392 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0421388213 | 4.74E-06 | 4.74E-06 | mr1108_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 |