Variant ID: vg1218089575 (JBrowse) | Variation Type: SNP |
Chromosome: chr12 | Position: 18089575 |
Reference Allele: T | Alternative Allele: A |
Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AGATAGCGATCTTTAGTCCCGGATTCGTAGTCCCGGTTGGAAAACCGGGACTACAGGGGGGTTACGAACCGGGACTAAAAAGCACTTCTCCACCAGTGTT[T/A]
GATGCGACTAATTAGCCCAATTTCCATGCATAGTCATGTACAGACTGCTGAGCTAAGTTATAATAATTGTAAACCATATATATGAGTTATTGTGGTTCAA
TTGAACCACAATAACTCATATATATGGTTTACAATTATTATAACTTAGCTCAGCAGTCTGTACATGACTATGCATGGAAATTGGGCTAATTAGTCGCATC[A/T]
AACACTGGTGGAGAAGTGCTTTTTAGTCCCGGTTCGTAACCCCCCTGTAGTCCCGGTTTTCCAACCGGGACTACGAATCCGGGACTAAAGATCGCTATCT
Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 95.00% | 4.70% | 0.02% | 0.25% | NA |
All Indica | 2759 | 97.10% | 2.50% | 0.00% | 0.43% | NA |
All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
Aus | 269 | 53.20% | 46.80% | 0.00% | 0.00% | NA |
Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica II | 465 | 97.00% | 2.20% | 0.00% | 0.86% | NA |
Indica III | 913 | 96.20% | 3.80% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 95.90% | 3.10% | 0.00% | 1.02% | NA |
Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 80.20% | 19.80% | 0.00% | 0.00% | NA |
Intermediate | 90 | 90.00% | 8.90% | 1.11% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg1218089575 | T -> DEL | N | N | silent_mutation | Average:34.466; most accessible tissue: Callus, score: 54.494 | N | N | N | N |
vg1218089575 | T -> A | LOC_Os12g30140.1 | upstream_gene_variant ; 1232.0bp to feature; MODIFIER | silent_mutation | Average:34.466; most accessible tissue: Callus, score: 54.494 | N | N | N | N |
vg1218089575 | T -> A | LOC_Os12g30130-LOC_Os12g30140 | intergenic_region ; MODIFIER | silent_mutation | Average:34.466; most accessible tissue: Callus, score: 54.494 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1218089575 | NA | 8.66E-07 | mr1006 | 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 |
vg1218089575 | NA | 7.88E-07 | mr1007 | 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 |
vg1218089575 | NA | 6.54E-07 | mr1052 | 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 |
vg1218089575 | NA | 5.03E-06 | mr1344_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 |
vg1218089575 | 1.92E-06 | NA | mr1526_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 |
vg1218089575 | NA | 4.99E-07 | mr1743_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 |