Variant ID: vg0314422629 (JBrowse) | Variation Type: INDEL |
Chromosome: chr03 | Position: 14422629 |
Reference Allele: T | Alternative Allele: A,TAC |
Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, A: 0.01, others allele: 0.00, population size: 204. )
TTAATGAAAGAGGCTGAAACCTGTTGATATATCTGGTTCATTGGCCACCATCGATTCCGTCCAAACTATTGTTCTTTGATGTGGAATGAATCCCTCCAAA[T/A,TAC]
ACACTTGATTATTGTTTCGAATTATAGTTGCAAAGTGTTAACTTTTGAAGTTAATTTTAACTTGCATGTTTGTGTAGTGATATATTACATATTGATCTAT
ATAGATCAATATGTAATATATCACTACACAAACATGCAAGTTAAAATTAACTTCAAAAGTTAACACTTTGCAACTATAATTCGAAACAATAATCAAGTGT[A/T,GTA]
TTTGGAGGGATTCATTCCACATCAAAGAACAATAGTTTGGACGGAATCGATGGTGGCCAATGAACCAGATATATCAACAGGTTTCAGCCTCTTTCATTAA
Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 49.60% | 31.90% | 11.21% | 7.30% | NA |
All Indica | 2759 | 18.50% | 51.50% | 18.16% | 11.78% | NA |
All Japonica | 1512 | 99.50% | 0.20% | 0.07% | 0.20% | NA |
Aus | 269 | 69.50% | 18.60% | 7.43% | 4.46% | NA |
Indica I | 595 | 16.00% | 42.70% | 23.36% | 17.98% | NA |
Indica II | 465 | 3.40% | 64.10% | 21.08% | 11.40% | NA |
Indica III | 913 | 25.20% | 46.70% | 17.20% | 10.95% | NA |
Indica Intermediate | 786 | 21.60% | 56.50% | 13.61% | 8.27% | NA |
Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 99.40% | 0.20% | 0.20% | 0.20% | NA |
Japonica Intermediate | 241 | 98.80% | 0.40% | 0.00% | 0.83% | NA |
VI/Aromatic | 96 | 92.70% | 6.20% | 0.00% | 1.04% | NA |
Intermediate | 90 | 58.90% | 27.80% | 8.89% | 4.44% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0314422629 | T -> A | LOC_Os03g25260.1 | upstream_gene_variant ; 2000.0bp to feature; MODIFIER | silent_mutation | Average:33.165; most accessible tissue: Minghui63 panicle, score: 50.413 | N | N | N | N |
vg0314422629 | T -> A | LOC_Os03g25240.1 | downstream_gene_variant ; 2267.0bp to feature; MODIFIER | silent_mutation | Average:33.165; most accessible tissue: Minghui63 panicle, score: 50.413 | N | N | N | N |
vg0314422629 | T -> A | LOC_Os03g25250.1 | downstream_gene_variant ; 353.0bp to feature; MODIFIER | silent_mutation | Average:33.165; most accessible tissue: Minghui63 panicle, score: 50.413 | N | N | N | N |
vg0314422629 | T -> A | LOC_Os03g25240-LOC_Os03g25250 | intergenic_region ; MODIFIER | silent_mutation | Average:33.165; most accessible tissue: Minghui63 panicle, score: 50.413 | N | N | N | N |
vg0314422629 | T -> DEL | N | N | silent_mutation | Average:33.165; most accessible tissue: Minghui63 panicle, score: 50.413 | N | N | N | N |
vg0314422629 | T -> TAC | LOC_Os03g25260.1 | upstream_gene_variant ; 1999.0bp to feature; MODIFIER | N | Average:33.165; most accessible tissue: Minghui63 panicle, score: 50.413 | N | N | N | N |
vg0314422629 | T -> TAC | LOC_Os03g25240.1 | downstream_gene_variant ; 2268.0bp to feature; MODIFIER | N | Average:33.165; most accessible tissue: Minghui63 panicle, score: 50.413 | N | N | N | N |
vg0314422629 | T -> TAC | LOC_Os03g25250.1 | downstream_gene_variant ; 352.0bp to feature; MODIFIER | N | Average:33.165; most accessible tissue: Minghui63 panicle, score: 50.413 | N | N | N | N |
vg0314422629 | T -> TAC | LOC_Os03g25240-LOC_Os03g25250 | intergenic_region ; MODIFIER | N | Average:33.165; most accessible tissue: Minghui63 panicle, score: 50.413 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0314422629 | NA | 3.08E-32 | mr1037 | 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 |
vg0314422629 | NA | 7.26E-09 | mr1037 | Ind_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 |
vg0314422629 | NA | 2.03E-36 | mr1064 | 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 |
vg0314422629 | NA | 2.25E-22 | mr1155 | 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 |
vg0314422629 | NA | 3.55E-11 | mr1713 | 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 |
vg0314422629 | NA | 5.58E-09 | mr1770 | 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 |
vg0314422629 | NA | 8.05E-07 | mr1785 | 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 |
vg0314422629 | NA | 1.90E-51 | mr1798 | 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 |
vg0314422629 | NA | 8.13E-09 | mr1798 | Ind_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 |
vg0314422629 | NA | 1.30E-22 | mr1888 | 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 |
vg0314422629 | 2.40E-06 | 2.40E-06 | mr1926 | Ind_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 |
vg0314422629 | NA | 2.32E-33 | mr1037_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 |
vg0314422629 | NA | 3.00E-08 | mr1798_2 | Ind_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 |