Variant ID: vg0625536742 (JBrowse) | Variation Type: SNP |
Chromosome: chr06 | Position: 25536742 |
Reference Allele: G | Alternative Allele: C |
Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 304. )
AGGATGATGGCGCCCCACCGCGAGCATGAATAGCTGCTTCCCATACACCTGGTACCCCCAGGATCTTCACCACCGTGCCAGGAAGGAGCTTCTCGATGTT[G/C]
TCACCCTCGAGGATGAGGAAGCTGATGGCGACAAGGTAGAGCTCGACTTATAAGACGAGGCCGATGGCCATCTAGCCGTAGCCGGCGAAGGCTAGGTACG
CGTACCTAGCCTTCGCCGGCTACGGCTAGATGGCCATCGGCCTCGTCTTATAAGTCGAGCTCTACCTTGTCGCCATCAGCTTCCTCATCCTCGAGGGTGA[C/G]
AACATCGAGAAGCTCCTTCCTGGCACGGTGGTGAAGATCCTGGGGGTACCAGGTGTATGGGAAGCAGCTATTCATGCTCGCGGTGGGGCGCCATCATCCT
Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 91.00% | 5.60% | 3.39% | 0.00% | NA |
All Indica | 2759 | 97.60% | 0.30% | 2.10% | 0.00% | NA |
All Japonica | 1512 | 77.20% | 16.20% | 6.55% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 96.10% | 0.00% | 3.87% | 0.00% | NA |
Indica II | 465 | 97.80% | 0.40% | 1.72% | 0.00% | NA |
Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 95.80% | 0.80% | 3.44% | 0.00% | NA |
Temperate Japonica | 767 | 89.60% | 2.00% | 8.47% | 0.00% | NA |
Tropical Japonica | 504 | 63.90% | 32.90% | 3.17% | 0.00% | NA |
Japonica Intermediate | 241 | 66.00% | 26.60% | 7.47% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 86.70% | 10.00% | 3.33% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0625536742 | G -> C | LOC_Os06g42480.1 | missense_variant ; p.Val26Leu; MODERATE | nonsynonymous_codon ; V26L | Average:69.979; most accessible tissue: Zhenshan97 young leaf, score: 83.199 | unknown | unknown | DELETERIOUS | 0.00 |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0625536742 | NA | 2.44E-06 | mr1114 | 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 |
vg0625536742 | NA | 2.94E-06 | mr1117 | 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 |
vg0625536742 | NA | 5.96E-06 | mr1119 | 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 |
vg0625536742 | 6.85E-07 | NA | mr1240 | 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 |
vg0625536742 | 1.51E-06 | 8.77E-08 | mr1240 | 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 |
vg0625536742 | NA | 8.44E-07 | mr1496 | 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 |
vg0625536742 | NA | 3.68E-07 | mr1602 | 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 |
vg0625536742 | 7.01E-07 | NA | mr1693 | 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 |