Variant ID: vg0408294799 (JBrowse) | Variation Type: SNP |
Chromosome: chr04 | Position: 8294799 |
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: 112. )
CAGGATGTGCCAGCCTCACACACGCAAGGACATGGCACACCCCGGTATAGATCCCGTTGAACGTCTCCTCTCCGACCCTGGCCGCGTGCTTGGAGGGGAT[C/T]
GCCTCCATCGCCGTTGCCAGTTCCGCAAGCGAAGACGTCAACGAGAACTCGTCGGGATTCGCCGGGATGGTGGCCTTGACGCCACACTCCCCGGCGAGCT
AGCTCGCCGGGGAGTGTGGCGTCAAGGCCACCATCCCGGCGAATCCCGACGAGTTCTCGTTGACGTCTTCGCTTGCGGAACTGGCAACGGCGATGGAGGC[G/A]
ATCCCCTCCAAGCACGCGGCCAGGGTCGGAGAGGAGACGTTCAACGGGATCTATACCGGGGTGTGCCATGTCCTTGCGTGTGTGAGGCTGGCACATCCTG
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 | 22.20% | 15.30% | 3.58% | 58.89% | NA |
All Indica | 2759 | 3.30% | 6.80% | 4.10% | 85.83% | NA |
All Japonica | 1512 | 61.80% | 24.10% | 1.46% | 12.57% | NA |
Aus | 269 | 1.90% | 32.30% | 7.43% | 58.36% | NA |
Indica I | 595 | 2.40% | 0.70% | 3.19% | 93.78% | NA |
Indica II | 465 | 3.20% | 25.60% | 4.73% | 66.45% | NA |
Indica III | 913 | 3.80% | 2.20% | 4.27% | 89.70% | NA |
Indica Intermediate | 786 | 3.40% | 5.60% | 4.20% | 86.77% | NA |
Temperate Japonica | 767 | 95.80% | 1.20% | 0.26% | 2.74% | NA |
Tropical Japonica | 504 | 6.50% | 65.30% | 3.37% | 24.80% | NA |
Japonica Intermediate | 241 | 69.30% | 11.20% | 1.24% | 18.26% | NA |
VI/Aromatic | 96 | 1.00% | 59.40% | 6.25% | 33.33% | NA |
Intermediate | 90 | 20.00% | 31.10% | 8.89% | 40.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0408294799 | C -> DEL | LOC_Os04g14780.1 | N | frameshift_variant | Average:17.471; most accessible tissue: Minghui63 root, score: 43.505 | N | N | N | N |
vg0408294799 | C -> T | LOC_Os04g14780.1 | synonymous_variant ; p.Ala280Ala; LOW | synonymous_codon | Average:17.471; most accessible tissue: Minghui63 root, score: 43.505 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0408294799 | 5.92E-06 | NA | mr1019 | 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 |
vg0408294799 | 1.41E-06 | NA | mr1023_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 |
vg0408294799 | 9.55E-06 | NA | mr1079_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 |
vg0408294799 | 3.17E-07 | NA | mr1132_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 |
vg0408294799 | 4.35E-06 | NA | mr1261_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 |
vg0408294799 | 1.24E-06 | NA | mr1390_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 |
vg0408294799 | 6.80E-06 | NA | mr1489_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 |
vg0408294799 | 1.68E-06 | NA | mr1490_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 |