Variant ID: vg0315146805 (JBrowse) | Variation Type: SNP |
Chromosome: chr03 | Position: 15146805 |
Reference Allele: T | Alternative Allele: C,A |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CAATCTTCTCCTTCACCCCTACTCTGTATCCTAATTCATCGTCCGCACAAAGATAAGCTGAATAAGAAGGGAGAAACACTACTAGAAAAATGCCTTTTTT[T/C,A]
AGGCGGTCAAAAGCGGCCCAGTCCCCCGCCTGTGAAAATCATCTCGACGAAAAAAAAATCGGTGCCACCCCACCCACACCCGTACCCACCTCTAGCCGAT
ATCGGCTAGAGGTGGGTACGGGTGTGGGTGGGGTGGCACCGATTTTTTTTTCGTCGAGATGATTTTCACAGGCGGGGGACTGGGCCGCTTTTGACCGCCT[A/G,T]
AAAAAAGGCATTTTTCTAGTAGTGTTTCTCCCTTCTTATTCAGCTTATCTTTGTGCGGACGATGAATTAGGATACAGAGTAGGGGTGAAGGAGAAGATTG
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 | 78.40% | 21.50% | 0.04% | 0.00% | A: 0.11% |
All Indica | 2759 | 99.70% | 0.30% | 0.04% | 0.00% | NA |
All Japonica | 1512 | 35.30% | 64.70% | 0.00% | 0.00% | NA |
Aus | 269 | 98.10% | 0.00% | 0.00% | 0.00% | A: 1.86% |
Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Indica III | 913 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 99.40% | 0.50% | 0.13% | 0.00% | NA |
Temperate Japonica | 767 | 3.90% | 96.10% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 80.60% | 19.40% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 40.70% | 59.30% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 92.70% | 7.30% | 0.00% | 0.00% | NA |
Intermediate | 90 | 75.60% | 23.30% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0315146805 | T -> C | LOC_Os03g26530.1 | upstream_gene_variant ; 3134.0bp to feature; MODIFIER | silent_mutation | Average:73.773; most accessible tissue: Callus, score: 86.869 | N | N | N | N |
vg0315146805 | T -> C | LOC_Os03g26520.1 | intron_variant ; MODIFIER | silent_mutation | Average:73.773; most accessible tissue: Callus, score: 86.869 | N | N | N | N |
vg0315146805 | T -> A | LOC_Os03g26530.1 | upstream_gene_variant ; 3134.0bp to feature; MODIFIER | silent_mutation | Average:73.773; most accessible tissue: Callus, score: 86.869 | N | N | N | N |
vg0315146805 | T -> A | LOC_Os03g26520.1 | intron_variant ; MODIFIER | silent_mutation | Average:73.773; most accessible tissue: Callus, score: 86.869 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0315146805 | NA | 8.56E-35 | Grain_thickness | 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 |
vg0315146805 | NA | 4.90E-55 | Grain_width | 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 |
vg0315146805 | NA | 4.02E-20 | mr1077 | 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 |
vg0315146805 | NA | 1.96E-06 | mr1077 | 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 |
vg0315146805 | NA | 6.12E-06 | mr1213 | 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 |
vg0315146805 | NA | 3.29E-17 | mr1308 | 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 |
vg0315146805 | NA | 2.29E-36 | mr1533 | 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 |
vg0315146805 | NA | 9.37E-09 | mr1575 | 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 |
vg0315146805 | NA | 6.10E-17 | mr1768 | 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 |
vg0315146805 | NA | 1.39E-43 | mr1771 | 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 |
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