Variant ID: vg0233356353 (JBrowse) | Variation Type: SNP |
Chromosome: chr02 | Position: 33356353 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AGATTGCGTCGTCACTGAGCAGCTGGCAGCAGCAACCAGGGAGATTGCGTCAGTGCCGAGCAGCTGTGATTGCCATGGAGTGAATTACGTCGGCGCCGGC[C/T]
GCTGGCGACACGCGATGCAGTTTCGATTTTTGGCTTTTCGCCAAATCGCTATCGCCCGGTCACCGATCGCTAAGCGCGTGCGCGTGAAGAGGACAAGAGG
CCTCTTGTCCTCTTCACGCGCACGCGCTTAGCGATCGGTGACCGGGCGATAGCGATTTGGCGAAAAGCCAAAAATCGAAACTGCATCGCGTGTCGCCAGC[G/A]
GCCGGCGCCGACGTAATTCACTCCATGGCAATCACAGCTGCTCGGCACTGACGCAATCTCCCTGGTTGCTGCTGCCAGCTGCTCAGTGACGACGCAATCT
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 | 98.50% | 1.20% | 0.23% | 0.00% | NA |
All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 95.50% | 3.80% | 0.66% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 91.50% | 7.30% | 1.17% | 0.00% | NA |
Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 98.80% | 0.80% | 0.41% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 97.80% | 1.10% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0233356353 | C -> T | LOC_Os02g54460.1 | missense_variant ; p.Arg42Cys; MODERATE | nonsynonymous_codon ; R42C | Average:62.935; most accessible tissue: Minghui63 root, score: 74.1 | unknown | unknown | DELETERIOUS | 0.00 |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0233356353 | NA | 1.33E-09 | Heading_date | Jap_All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
vg0233356353 | 3.07E-06 | 3.07E-06 | mr1038 | 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 |
vg0233356353 | NA | 2.12E-07 | mr1354 | 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 |
vg0233356353 | 5.08E-07 | 5.08E-07 | mr1389 | 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 |
vg0233356353 | 5.66E-06 | 2.47E-06 | mr1038_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 |
vg0233356353 | NA | 5.17E-08 | mr1354_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 |
vg0233356353 | 5.74E-07 | 5.74E-07 | mr1389_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 |