Variant ID: vg0607152342 (JBrowse) | Variation Type: SNP |
Chromosome: chr06 | Position: 7152342 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.00, others allele: 0.00, population size: 268. )
ATCCTTTAATATTGAGAATGTCACATTTTTAAGTGCTCACGTTTTTTAAACATCCACTCAGCATTTCAACTTTAAATTTGAGAAGAAAGTCAATATAGTA[C/T]
GAAACCATCAGAAAGAAGTAGGAGAGAAATTTGGTTGCATGTGATATCATTCATACAAAAAAGTACTTACCCCATCAGTAATCCAATATAAATATTGTAT
ATACAATATTTATATTGGATTACTGATGGGGTAAGTACTTTTTTGTATGAATGATATCACATGCAACCAAATTTCTCTCCTACTTCTTTCTGATGGTTTC[G/A]
TACTATATTGACTTTCTTCTCAAATTTAAAGTTGAAATGCTGAGTGGATGTTTAAAAAACGTGAGCACTTAAAAATGTGACATTCTCAATATTAAAGGAT
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 | 78.20% | 20.10% | 1.63% | 0.00% | NA |
All Indica | 2759 | 92.40% | 7.60% | 0.04% | 0.00% | NA |
All Japonica | 1512 | 47.90% | 47.20% | 4.83% | 0.00% | NA |
Aus | 269 | 95.90% | 3.70% | 0.37% | 0.00% | NA |
Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Indica II | 465 | 97.20% | 2.80% | 0.00% | 0.00% | NA |
Indica III | 913 | 88.20% | 11.80% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 88.70% | 11.20% | 0.13% | 0.00% | NA |
Temperate Japonica | 767 | 61.80% | 30.80% | 7.43% | 0.00% | NA |
Tropical Japonica | 504 | 27.20% | 70.40% | 2.38% | 0.00% | NA |
Japonica Intermediate | 241 | 47.30% | 51.00% | 1.66% | 0.00% | NA |
VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
Intermediate | 90 | 80.00% | 17.80% | 2.22% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0607152342 | C -> T | LOC_Os06g13050.1 | intron_variant ; MODIFIER | silent_mutation | Average:35.388; most accessible tissue: Callus, score: 49.481 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0607152342 | NA | 4.54E-06 | mr1002 | 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 |
vg0607152342 | NA | 8.29E-06 | mr1180 | 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 |
vg0607152342 | NA | 8.38E-07 | mr1183 | 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 |
vg0607152342 | NA | 1.34E-08 | mr1354 | 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 |
vg0607152342 | NA | 5.17E-07 | mr1408 | 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 |
vg0607152342 | NA | 6.27E-07 | mr1503 | 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 |
vg0607152342 | NA | 3.95E-09 | mr1794 | 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 |
vg0607152342 | NA | 1.53E-06 | mr1183_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 |
vg0607152342 | NA | 9.49E-11 | mr1794_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 |