Variant ID: vg0823106771 (JBrowse) | Variation Type: SNP |
Chromosome: chr08 | Position: 23106771 |
Reference Allele: G | Alternative Allele: C |
Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, G: 0.01, others allele: 0.00, population size: 82. )
TCCGCCTACTCCATTCATCCAGGAAGTACGAAGATGTACCAAGATATCAAGGCATACTTCTGGTGGGCTGGAATGAAGCGAGATGTCACAGAATACGTAG[G/C]
CTTGTGTGACATTTGCCAAAGAGTCAAGGCAGAGCATCATTGACCAGCTGGTCTGCTGCAACCCGTACCGATTCCCGAGTGGAAATGGGAAGAGATCGGA
TCCGATCTCTTCCCATTTCCACTCGGGAATCGGTACGGGTTGCAGCAGACCAGCTGGTCAATGATGCTCTGCCTTGACTCTTTGGCAAATGTCACACAAG[C/G]
CTACGTATTCTGTGACATCTCGCTTCATTCCAGCCCACCAGAAGTATGCCTTGATATCTTGGTACATCTTCGTACTTCCTGGATGAATGGAGTAGGCGGA
Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 17.00% | 14.60% | 18.54% | 49.87% | NA |
All Indica | 2759 | 1.00% | 1.00% | 17.25% | 80.75% | NA |
All Japonica | 1512 | 49.20% | 42.70% | 7.08% | 1.06% | NA |
Aus | 269 | 2.60% | 1.10% | 76.95% | 19.33% | NA |
Indica I | 595 | 0.50% | 0.80% | 8.91% | 89.75% | NA |
Indica II | 465 | 1.30% | 1.50% | 32.47% | 64.73% | NA |
Indica III | 913 | 0.80% | 0.40% | 11.06% | 87.73% | NA |
Indica Intermediate | 786 | 1.50% | 1.40% | 21.76% | 75.32% | NA |
Temperate Japonica | 767 | 17.50% | 72.40% | 8.87% | 1.30% | NA |
Tropical Japonica | 504 | 91.70% | 4.40% | 3.37% | 0.60% | NA |
Japonica Intermediate | 241 | 61.40% | 28.20% | 9.13% | 1.24% | NA |
VI/Aromatic | 96 | 6.20% | 1.00% | 68.75% | 23.96% | NA |
Intermediate | 90 | 22.20% | 13.30% | 22.22% | 42.22% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0823106771 | G -> C | LOC_Os08g36620.1 | splice_region_variant&intron_variant ; LOW | silent_mutation | Average:9.143; most accessible tissue: Callus, score: 29.731 | N | N | N | N |
vg0823106771 | G -> DEL | N | N | silent_mutation | Average:9.143; most accessible tissue: Callus, score: 29.731 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0823106771 | NA | 3.35E-23 | mr1115 | 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 |
vg0823106771 | NA | 1.58E-07 | mr1229 | 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 |
vg0823106771 | NA | 9.16E-09 | mr1229 | 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 |
vg0823106771 | NA | 1.46E-06 | mr1252 | 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 |
vg0823106771 | NA | 5.00E-07 | mr1763 | 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 |
vg0823106771 | NA | 9.31E-09 | mr1880 | 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 |
vg0823106771 | NA | 1.07E-11 | mr1880 | 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 |
vg0823106771 | NA | 1.23E-06 | mr1977 | 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 |
vg0823106771 | 5.60E-06 | NA | mr1181_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 |
vg0823106771 | NA | 5.24E-08 | mr1952_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 |
vg0823106771 | NA | 1.59E-09 | mr1952_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 |