Variant ID: vg1005044043 (JBrowse) | Variation Type: SNP |
Chromosome: chr10 | Position: 5044043 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, others allele: 0.00, population size: 68. )
TGTACTAGACAGCTTCACATATTTATGATACTAATATATTGATTAACTTCAATGCATGCAGTTGCCAAGATTAGAACGTCGAACAAGCTTTGACGATACA[G/A]
ACATCACAAATGTCCAGCGTGATCTGTGCCATTTCATCCACCATGAGTGCTGTCATGTGAAAGGAGATTTCTTCGACCCAGAGGGTGCCCTAGCGACAAG
CTTGTCGCTAGGGCACCCTCTGGGTCGAAGAAATCTCCTTTCACATGACAGCACTCATGGTGGATGAAATGGCACAGATCACGCTGGACATTTGTGATGT[C/T]
TGTATCGTCAAAGCTTGTTCGACGTTCTAATCTTGGCAACTGCATGCATTGAAGTTAATCAATATATTAGTATCATAAATATGTGAAGCTGTCTAGTACA
Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 64.10% | 2.90% | 0.66% | 32.40% | NA |
All Indica | 2759 | 56.60% | 4.90% | 0.80% | 37.73% | NA |
All Japonica | 1512 | 71.40% | 0.00% | 0.53% | 28.04% | NA |
Aus | 269 | 85.10% | 0.00% | 0.37% | 14.50% | NA |
Indica I | 595 | 49.90% | 16.10% | 1.51% | 32.44% | NA |
Indica II | 465 | 51.00% | 2.80% | 0.65% | 45.59% | NA |
Indica III | 913 | 62.50% | 0.20% | 0.66% | 36.58% | NA |
Indica Intermediate | 786 | 58.10% | 2.90% | 0.51% | 38.42% | NA |
Temperate Japonica | 767 | 80.80% | 0.00% | 0.13% | 19.04% | NA |
Tropical Japonica | 504 | 59.30% | 0.00% | 0.79% | 39.88% | NA |
Japonica Intermediate | 241 | 66.80% | 0.00% | 1.24% | 31.95% | NA |
VI/Aromatic | 96 | 91.70% | 0.00% | 0.00% | 8.33% | NA |
Intermediate | 90 | 77.80% | 1.10% | 0.00% | 21.11% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg1005044043 | G -> A | LOC_Os10g09330.1 | missense_variant ; p.Asp32Asn; MODERATE | nonsynonymous_codon ; D32N | Average:15.426; most accessible tissue: Callus, score: 49.421 | benign | 1.269 | DELETERIOUS | 0.03 |
vg1005044043 | G -> DEL | LOC_Os10g09330.1 | N | frameshift_variant | Average:15.426; most accessible tissue: Callus, score: 49.421 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1005044043 | 8.47E-07 | 8.38E-08 | mr1519_2 | 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 |