Variant ID: vg0905973876 (JBrowse) | Variation Type: SNP |
Chromosome: chr09 | Position: 5973876 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.62, A: 0.38, others allele: 0.00, population size: 103. )
GTCAGACCGGGCACCGGTCAGACTGAGGGTACAGTGGCGGTCAGACCAGCTACTGTACTTCGGTCAGACCGGCCTCGCAGAGATTTTTCTAAAATTCTCA[G/A]
ACTGTTTTTGCACGTGGATATATGCCTATTAGATCTACTGGTCATGTGTCTCAGTACTGGATTCCTAAATTTTTATTATCTAACCCCAGTATTGAGGCTT
AAGCCTCAATACTGGGGTTAGATAATAAAAATTTAGGAATCCAGTACTGAGACACATGACCAGTAGATCTAATAGGCATATATCCACGTGCAAAAACAGT[C/T]
TGAGAATTTTAGAAAAATCTCTGCGAGGCCGGTCTGACCGAAGTACAGTAGCTGGTCTGACCGCCACTGTACCCTCAGTCTGACCGGTGCCCGGTCTGAC
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 | 61.90% | 38.10% | 0.00% | 0.00% | NA |
All Indica | 2759 | 87.80% | 12.20% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 6.50% | 93.50% | 0.00% | 0.00% | NA |
Aus | 269 | 97.40% | 2.60% | 0.00% | 0.00% | NA |
Indica I | 595 | 83.40% | 16.60% | 0.00% | 0.00% | NA |
Indica II | 465 | 94.00% | 6.00% | 0.00% | 0.00% | NA |
Indica III | 913 | 87.70% | 12.30% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 87.70% | 12.30% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 1.60% | 98.40% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 2.60% | 97.40% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 30.30% | 69.70% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 94.80% | 5.20% | 0.00% | 0.00% | NA |
Intermediate | 90 | 56.70% | 43.30% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0905973876 | G -> A | LOC_Os09g10890.1 | intron_variant ; MODIFIER | silent_mutation | Average:55.739; most accessible tissue: Minghui63 panicle, score: 77.956 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0905973876 | NA | 6.25E-17 | mr1116 | 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 |
vg0905973876 | NA | 1.51E-06 | mr1242 | 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 |
vg0905973876 | NA | 7.99E-17 | mr1114_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 |
vg0905973876 | NA | 4.48E-06 | mr1240_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 |
vg0905973876 | 7.07E-07 | 1.85E-09 | mr1350_2 | 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 |