Variant ID: vg0324209979 (JBrowse) | Variation Type: SNP |
Chromosome: chr03 | Position: 24209979 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 272. )
ACTTAACCAACATATTTTAATATTGACAAAGTCACCGCAGTCATCTCGCTATCAACAGGCACGTCGATCACCTGCCACTAAAACAATTAATAGCTACAGA[C/T]
ATGAGCGTACTCATGTCAAATTTAGAACTTGAACTCTTATCTAGACGAGCAGGTTTCATCACAAGAAATCTAAGCAGCTGAGCTACGCTAAATTCGTGAA
TTCACGAATTTAGCGTAGCTCAGCTGCTTAGATTTCTTGTGATGAAACCTGCTCGTCTAGATAAGAGTTCAAGTTCTAAATTTGACATGAGTACGCTCAT[G/A]
TCTGTAGCTATTAATTGTTTTAGTGGCAGGTGATCGACGTGCCTGTTGATAGCGAGATGACTGCGGTGACTTTGTCAATATTAAAATATGTTGGTTAAGT
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 | 73.20% | 24.80% | 1.69% | 0.36% | NA |
All Indica | 2759 | 98.40% | 1.20% | 0.04% | 0.33% | NA |
All Japonica | 1512 | 32.50% | 62.30% | 4.89% | 0.33% | NA |
Aus | 269 | 62.10% | 37.90% | 0.00% | 0.00% | NA |
Indica I | 595 | 99.70% | 0.20% | 0.00% | 0.17% | NA |
Indica II | 465 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
Indica III | 913 | 99.10% | 0.40% | 0.00% | 0.44% | NA |
Indica Intermediate | 786 | 96.30% | 3.10% | 0.13% | 0.51% | NA |
Temperate Japonica | 767 | 57.20% | 36.00% | 6.65% | 0.13% | NA |
Tropical Japonica | 504 | 4.60% | 92.50% | 2.58% | 0.40% | NA |
Japonica Intermediate | 241 | 12.00% | 83.00% | 4.15% | 0.83% | NA |
VI/Aromatic | 96 | 25.00% | 75.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 66.70% | 24.40% | 5.56% | 3.33% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0324209979 | C -> T | LOC_Os03g43410.1 | upstream_gene_variant ; 2575.0bp to feature; MODIFIER | silent_mutation | Average:54.679; most accessible tissue: Minghui63 root, score: 84.323 | N | N | N | N |
vg0324209979 | C -> T | LOC_Os03g43400-LOC_Os03g43410 | intergenic_region ; MODIFIER | silent_mutation | Average:54.679; most accessible tissue: Minghui63 root, score: 84.323 | N | N | N | N |
vg0324209979 | C -> DEL | N | N | silent_mutation | Average:54.679; most accessible tissue: Minghui63 root, score: 84.323 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0324209979 | NA | 2.05E-10 | mr1486 | 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 |
vg0324209979 | NA | 4.48E-07 | mr1548 | 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 |
vg0324209979 | NA | 1.48E-07 | mr1010_2 | 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 |
vg0324209979 | NA | 2.88E-08 | mr1084_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 |
vg0324209979 | NA | 1.81E-07 | mr1205_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 |
vg0324209979 | NA | 8.26E-07 | mr1263_2 | 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 |
vg0324209979 | NA | 7.68E-06 | mr1379_2 | 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 |
vg0324209979 | NA | 4.30E-16 | mr1454_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 |
vg0324209979 | NA | 3.36E-15 | mr1486_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 |
vg0324209979 | NA | 3.52E-09 | mr1588_2 | 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 |