Variant ID: vg1105865316 (JBrowse) | Variation Type: SNP |
Chromosome: chr11 | Position: 5865316 |
Reference Allele: A | Alternative Allele: T |
Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.94, T: 0.05, others allele: 0.00, population size: 241. )
ATAATGCCACATCGGCATAAGCAAAATGATTCCTCTGCATTATATTCCTCCAGGAAGAACATTGCGCTGTAGCCTTTTATAAACAAAACACACGATAGTA[A/T]
TAATTAATTACCTCACCAATGATAGCTTCTTTCTCGTTAATTTGATTGATGATTTCCACTATATTAGGCCTATTTTCCCTATCAGTCTCCATGCATTTCA
TGAAATGCATGGAGACTGATAGGGAAAATAGGCCTAATATAGTGGAAATCATCAATCAAATTAACGAGAAAGAAGCTATCATTGGTGAGGTAATTAATTA[T/A]
TACTATCGTGTGTTTTGTTTATAAAAGGCTACAGCGCAATGTTCTTCCTGGAGGAATATAATGCAGAGGAATCATTTTGCTTATGCCGATGTGGCATTAT
Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 88.50% | 11.40% | 0.08% | 0.00% | NA |
All Indica | 2759 | 92.60% | 7.20% | 0.14% | 0.00% | NA |
All Japonica | 1512 | 93.50% | 6.50% | 0.00% | 0.00% | NA |
Aus | 269 | 16.70% | 83.30% | 0.00% | 0.00% | NA |
Indica I | 595 | 97.50% | 2.40% | 0.17% | 0.00% | NA |
Indica II | 465 | 98.70% | 1.30% | 0.00% | 0.00% | NA |
Indica III | 913 | 86.50% | 13.40% | 0.11% | 0.00% | NA |
Indica Intermediate | 786 | 92.40% | 7.40% | 0.25% | 0.00% | NA |
Temperate Japonica | 767 | 93.70% | 6.30% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 95.60% | 4.40% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 88.40% | 11.60% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 87.50% | 12.50% | 0.00% | 0.00% | NA |
Intermediate | 90 | 92.20% | 7.80% | 0.00% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg1105865316 | A -> T | LOC_Os11g10670-LOC_Os11g10710 | intergenic_region ; MODIFIER | silent_mutation | Average:37.452; most accessible tissue: Callus, score: 80.287 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1105865316 | NA | 2.98E-08 | mr1465 | 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 |
vg1105865316 | 4.59E-06 | NA | mr1203_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 |
vg1105865316 | 1.16E-07 | NA | mr1613_2 | 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 |
vg1105865316 | 1.41E-06 | NA | mr1613_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 |