Variant ID: vg1010554538 (JBrowse) | Variation Type: SNP |
Chromosome: chr10 | Position: 10554538 |
Reference Allele: A | Alternative Allele: G |
Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CGAACACGAGGGAAAGGCGTGATTCCCTGGAAGATTAGATTCAAGGAGGACATCCACACGTACAGGAGTTGGATGAGGAGTAAGAGAGATATCGAGGCGA[A/G]
GATTGCAAATCTTGAGTACAGGGTATCGAGCTACGAGCTCAGCATGCAAGAGGAGGTGGCAAGGAAGGTGGATGAATGCATGGCCGCACATCGGTCCCAG
CTGGGACCGATGTGCGGCCATGCATTCATCCACCTTCCTTGCCACCTCCTCTTGCATGCTGAGCTCGTAGCTCGATACCCTGTACTCAAGATTTGCAATC[T/C]
TCGCCTCGATATCTCTCTTACTCCTCATCCAACTCCTGTACGTGTGGATGTCCTCCTTGAATCTAATCTTCCAGGGAATCACGCCTTTCCCTCGTGTTCG
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 | 23.00% | 0.80% | 4.44% | 71.69% | NA |
All Indica | 2759 | 2.90% | 1.40% | 5.18% | 90.50% | NA |
All Japonica | 1512 | 62.80% | 0.00% | 2.65% | 34.52% | NA |
Aus | 269 | 3.70% | 0.00% | 5.95% | 90.33% | NA |
Indica I | 595 | 1.80% | 3.90% | 3.19% | 91.09% | NA |
Indica II | 465 | 1.90% | 1.10% | 3.23% | 93.76% | NA |
Indica III | 913 | 3.50% | 0.00% | 6.24% | 90.25% | NA |
Indica Intermediate | 786 | 3.40% | 1.50% | 6.62% | 88.42% | NA |
Temperate Japonica | 767 | 77.10% | 0.00% | 4.56% | 18.38% | NA |
Tropical Japonica | 504 | 48.40% | 0.00% | 0.20% | 51.39% | NA |
Japonica Intermediate | 241 | 47.70% | 0.00% | 1.66% | 50.62% | NA |
VI/Aromatic | 96 | 16.70% | 0.00% | 8.33% | 75.00% | NA |
Intermediate | 90 | 36.70% | 0.00% | 3.33% | 60.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg1010554538 | A -> G | LOC_Os10g20810.1 | missense_variant ; p.Lys150Arg; MODERATE | nonsynonymous_codon ; K150R | Average:9.744; most accessible tissue: Callus, score: 30.695 | unknown | unknown | DELETERIOUS | 0.00 |
vg1010554538 | A -> DEL | LOC_Os10g20810.1 | N | frameshift_variant | Average:9.744; most accessible tissue: Callus, score: 30.695 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1010554538 | NA | 1.03E-07 | mr1162 | 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 |
vg1010554538 | 8.37E-06 | 8.37E-06 | mr1551 | Ind_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 |
vg1010554538 | 9.66E-07 | NA | mr1679 | Ind_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 |
vg1010554538 | 2.69E-07 | 1.75E-07 | mr1768 | Ind_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 |
vg1010554538 | NA | 1.43E-07 | mr1837_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 |