Variant ID: vg0718051702 (JBrowse) | Variation Type: SNP |
Chromosome: chr07 | Position: 18051702 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, T: 0.07, others allele: 0.00, population size: 81. )
CAGTAATCAAACGGCGGTGAGTAAGGTAGCTAGACATGTCCCACAATGTGACTTATCCATAGATGGTGATCGGCAACGAAGAAAACCAGAACAACGGGAA[C/T]
ACGACCAGCAACGGCATGGTCCCATAGAGAGAGAAACGGCAACGATGATCTCTTGTGGTGAACACAGCCGGGTGAGTACATCAAAACGTGTTCACGGACA
TGTCCGTGAACACGTTTTGATGTACTCACCCGGCTGTGTTCACCACAAGAGATCATCGTTGCCGTTTCTCTCTCTATGGGACCATGCCGTTGCTGGTCGT[G/A]
TTCCCGTTGTTCTGGTTTTCTTCGTTGCCGATCACCATCTATGGATAAGTCACATTGTGGGACATGTCTAGCTACCTTACTCACCGCCGTTTGATTACTG
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 | 49.50% | 29.40% | 9.54% | 11.57% | NA |
All Indica | 2759 | 44.20% | 46.50% | 2.28% | 7.00% | NA |
All Japonica | 1512 | 63.00% | 0.70% | 22.29% | 14.02% | NA |
Aus | 269 | 9.30% | 27.10% | 13.75% | 49.81% | NA |
Indica I | 595 | 83.00% | 15.60% | 0.17% | 1.18% | NA |
Indica II | 465 | 18.50% | 77.60% | 1.72% | 2.15% | NA |
Indica III | 913 | 31.50% | 56.10% | 3.83% | 8.54% | NA |
Indica Intermediate | 786 | 44.80% | 40.30% | 2.42% | 12.47% | NA |
Temperate Japonica | 767 | 66.90% | 0.50% | 22.03% | 10.56% | NA |
Tropical Japonica | 504 | 54.20% | 0.80% | 26.98% | 18.06% | NA |
Japonica Intermediate | 241 | 68.90% | 1.20% | 13.28% | 16.60% | NA |
VI/Aromatic | 96 | 88.50% | 1.00% | 8.33% | 2.08% | NA |
Intermediate | 90 | 63.30% | 23.30% | 6.67% | 6.67% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0718051702 | C -> DEL | N | N | silent_mutation | Average:22.939; most accessible tissue: Zhenshan97 flower, score: 45.068 | N | N | N | N |
vg0718051702 | C -> T | LOC_Os07g30510.1 | upstream_gene_variant ; 592.0bp to feature; MODIFIER | silent_mutation | Average:22.939; most accessible tissue: Zhenshan97 flower, score: 45.068 | N | N | N | N |
vg0718051702 | C -> T | LOC_Os07g30510-LOC_Os07g30530 | intergenic_region ; MODIFIER | silent_mutation | Average:22.939; most accessible tissue: Zhenshan97 flower, score: 45.068 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0718051702 | 7.86E-07 | 2.71E-07 | mr1211 | 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 |
vg0718051702 | NA | 6.20E-06 | mr1184_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 |