Variant ID: vg0100100017 (JBrowse) | Variation Type: SNP |
Chromosome: chr01 | Position: 100017 |
Reference Allele: T | Alternative Allele: C |
Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.63, T: 0.38, others allele: 0.00, population size: 94. )
TGTCGCTTCAATCCACTTAGTGAATTTATCAATCGCCACGAATAGGAACTTGTAGCCGCCCTGTCCTCGTGGGAATGGGCCGAGTATATCTAGCCCCCAG[T/C]
ACGAGAACGGCCAAGTGAGAGGGATGGTCTGGAGTGCTTGCGCTGGTAGCCTTGTGTGTTTACTGTGGAATTGACAGCTTCACACCGCTAAACCATGTCG
CGACATGGTTTAGCGGTGTGAAGCTGTCAATTCCACAGTAAACACACAAGGCTACCAGCGCAAGCACTCCAGACCATCCCTCTCACTTGGCCGTTCTCGT[A/G]
CTGGGGGCTAGATATACTCGGCCCATTCCCACGAGGACAGGGCGGCTACAAGTTCCTATTCGTGGCGATTGATAAATTCACTAAGTGGATTGAAGCGACA
Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 75.20% | 24.80% | 0.00% | 0.00% | NA |
All Indica | 2759 | 68.90% | 31.10% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 97.60% | 2.40% | 0.00% | 0.00% | NA |
Aus | 269 | 9.30% | 90.70% | 0.00% | 0.00% | NA |
Indica I | 595 | 28.40% | 71.60% | 0.00% | 0.00% | NA |
Indica II | 465 | 96.60% | 3.40% | 0.00% | 0.00% | NA |
Indica III | 913 | 85.90% | 14.10% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 63.40% | 36.60% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 93.80% | 6.20% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 82.30% | 17.70% | 0.00% | 0.00% | NA |
Intermediate | 90 | 82.20% | 17.80% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0100100017 | T -> C | LOC_Os01g01200.1 | downstream_gene_variant ; 1459.0bp to feature; MODIFIER | silent_mutation | Average:42.242; most accessible tissue: Minghui63 root, score: 63.193 | N | N | N | N |
vg0100100017 | T -> C | LOC_Os01g01210.1 | intron_variant ; MODIFIER | silent_mutation | Average:42.242; most accessible tissue: Minghui63 root, score: 63.193 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0100100017 | NA | 2.22E-10 | mr1662 | 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 |
vg0100100017 | 3.18E-06 | NA | mr1718 | 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 |
vg0100100017 | NA | 3.21E-06 | mr1265_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 |
vg0100100017 | NA | 8.86E-07 | mr1528_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 |