Variant ID: vg0335559333 (JBrowse) | Variation Type: SNP |
Chromosome: chr03 | Position: 35559333 |
Reference Allele: A | Alternative Allele: G |
Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GTCTTAAAAAAAAAGGCCAAAAAAGCATGCAAGATGAAACTTGTTTATAGCCCGGGTTTAGTTCTCAACTTTTTCTTCAAACTTTCAACTTTTCTATCAC[A/G]
TCAAAACTTTTCTACACACATAAATTTACAACTTTTTTCTTCAAACTTTCAATTTTAATCAAATTTCCAATTTTGATGTGTAACTAAACACACCATAGAT
ATCTATGGTGTGTTTAGTTACACATCAAAATTGGAAATTTGATTAAAATTGAAAGTTTGAAGAAAAAAGTTGTAAATTTATGTGTGTAGAAAAGTTTTGA[T/C]
GTGATAGAAAAGTTGAAAGTTTGAAGAAAAAGTTGAGAACTAAACCCGGGCTATAAACAAGTTTCATCTTGCATGCTTTTTTGGCCTTTTTTTTTAAGAC
Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 95.20% | 4.20% | 0.61% | 0.00% | NA |
All Indica | 2759 | 99.90% | 0.00% | 0.11% | 0.00% | NA |
All Japonica | 1512 | 85.40% | 12.90% | 1.72% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 99.80% | 0.00% | 0.17% | 0.00% | NA |
Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica III | 913 | 99.90% | 0.00% | 0.11% | 0.00% | NA |
Indica Intermediate | 786 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
Temperate Japonica | 767 | 98.70% | 0.00% | 1.30% | 0.00% | NA |
Tropical Japonica | 504 | 60.10% | 37.30% | 2.58% | 0.00% | NA |
Japonica Intermediate | 241 | 95.90% | 2.90% | 1.24% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 97.80% | 2.20% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0335559333 | A -> G | LOC_Os03g62850.1 | upstream_gene_variant ; 1285.0bp to feature; MODIFIER | silent_mutation | Average:41.137; most accessible tissue: Zhenshan97 flower, score: 65.596 | N | N | N | N |
vg0335559333 | A -> G | LOC_Os03g62850.2 | upstream_gene_variant ; 1285.0bp to feature; MODIFIER | silent_mutation | Average:41.137; most accessible tissue: Zhenshan97 flower, score: 65.596 | N | N | N | N |
vg0335559333 | A -> G | LOC_Os03g62870.1 | downstream_gene_variant ; 3421.0bp to feature; MODIFIER | silent_mutation | Average:41.137; most accessible tissue: Zhenshan97 flower, score: 65.596 | N | N | N | N |
vg0335559333 | A -> G | LOC_Os03g62870.2 | downstream_gene_variant ; 3421.0bp to feature; MODIFIER | silent_mutation | Average:41.137; most accessible tissue: Zhenshan97 flower, score: 65.596 | N | N | N | N |
vg0335559333 | A -> G | LOC_Os03g62870.3 | downstream_gene_variant ; 3421.0bp to feature; MODIFIER | silent_mutation | Average:41.137; most accessible tissue: Zhenshan97 flower, score: 65.596 | N | N | N | N |
vg0335559333 | A -> G | LOC_Os03g62870.4 | downstream_gene_variant ; 3421.0bp to feature; MODIFIER | silent_mutation | Average:41.137; most accessible tissue: Zhenshan97 flower, score: 65.596 | N | N | N | N |
vg0335559333 | A -> G | LOC_Os03g62860.1 | intron_variant ; MODIFIER | silent_mutation | Average:41.137; most accessible tissue: Zhenshan97 flower, score: 65.596 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0335559333 | 2.54E-06 | 1.26E-08 | mr1422 | 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 |
vg0335559333 | NA | 6.29E-07 | mr1422_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 |
vg0335559333 | NA | 1.29E-06 | mr1850_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 |
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