Variant ID: vg1213936261 (JBrowse) | Variation Type: SNP |
Chromosome: chr12 | Position: 13936261 |
Reference Allele: C | Alternative Allele: G |
Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, G: 0.05, others allele: 0.00, population size: 109. )
AGGTTTAGAACCAGGCAGAGGTGCAGCCCACCTCCTGCCGACTATATCATACGCGATGTGCAGTAAAAACCCTAAAAAAATTTTCCCTAACTACACCGAA[C/G]
AAAACTTCAAAGCACACACATCATGTGGTTTCAGATCCAGGATGCTTTACTCGACATTGGGCAAAATCAACTCAAAAACATATACCCAGTAAACTCCAAA
TTTGGAGTTTACTGGGTATATGTTTTTGAGTTGATTTTGCCCAATGTCGAGTAAAGCATCCTGGATCTGAAACCACATGATGTGTGTGCTTTGAAGTTTT[G/C]
TTCGGTGTAGTTAGGGAAAATTTTTTTAGGGTTTTTACTGCACATCGCGTATGATATAGTCGGCAGGAGGTGGGCTGCACCTCTGCCTGGTTCTAAACCT
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 | 53.30% | 19.00% | 27.66% | 0.00% | NA |
All Indica | 2759 | 47.80% | 26.80% | 25.37% | 0.00% | NA |
All Japonica | 1512 | 57.10% | 8.30% | 34.66% | 0.00% | NA |
Aus | 269 | 82.50% | 2.60% | 14.87% | 0.00% | NA |
Indica I | 595 | 29.10% | 40.80% | 30.08% | 0.00% | NA |
Indica II | 465 | 70.80% | 10.50% | 18.71% | 0.00% | NA |
Indica III | 913 | 46.90% | 29.20% | 23.88% | 0.00% | NA |
Indica Intermediate | 786 | 49.50% | 23.00% | 27.48% | 0.00% | NA |
Temperate Japonica | 767 | 84.20% | 2.50% | 13.30% | 0.00% | NA |
Tropical Japonica | 504 | 24.60% | 14.90% | 60.52% | 0.00% | NA |
Japonica Intermediate | 241 | 38.60% | 12.90% | 48.55% | 0.00% | NA |
VI/Aromatic | 96 | 67.70% | 13.50% | 18.75% | 0.00% | NA |
Intermediate | 90 | 57.80% | 14.40% | 27.78% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg1213936261 | C -> G | LOC_Os12g24410.1 | upstream_gene_variant ; 3699.0bp to feature; MODIFIER | silent_mutation | Average:29.709; most accessible tissue: Minghui63 young leaf, score: 42.042 | N | N | N | N |
vg1213936261 | C -> G | LOC_Os12g24430.1 | upstream_gene_variant ; 2534.0bp to feature; MODIFIER | silent_mutation | Average:29.709; most accessible tissue: Minghui63 young leaf, score: 42.042 | N | N | N | N |
vg1213936261 | C -> G | LOC_Os12g24420.1 | downstream_gene_variant ; 280.0bp to feature; MODIFIER | silent_mutation | Average:29.709; most accessible tissue: Minghui63 young leaf, score: 42.042 | N | N | N | N |
vg1213936261 | C -> G | LOC_Os12g24410-LOC_Os12g24420 | intergenic_region ; MODIFIER | silent_mutation | Average:29.709; most accessible tissue: Minghui63 young leaf, score: 42.042 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1213936261 | NA | 4.41E-06 | mr1364 | 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 |
vg1213936261 | NA | 3.48E-09 | mr1401 | 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 |
vg1213936261 | NA | 2.51E-06 | mr1443 | 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 |
vg1213936261 | NA | 1.09E-06 | 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 |