Variant ID: vg1014304342 (JBrowse) | Variation Type: SNP |
Chromosome: chr10 | Position: 14304342 |
Reference Allele: C | Alternative Allele: A |
Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 104. )
GTTAATTACATGTCTGATGCCGATCATATCGGAGTTCCAGCGTCTCGTCACGAGGGAAGGTTGTCGGGTGTTGGCACAATCGGAAGGAAAAGAATTAGGC[C/A]
CGATCAAGCATCGTACGCGCAGGCTCATTACGCTATGCTCCAACATATGGCAGAAGTTGGCCCATACTTTGAGGAGCACCTAGCGAAAATCCGAGATGAG
CTCATCTCGGATTTTCGCTAGGTGCTCCTCAAAGTATGGGCCAACTTCTGCCATATGTTGGAGCATAGCGTAATGAGCCTGCGCGTACGATGCTTGATCG[G/T]
GCCTAATTCTTTTCCTTCCGATTGTGCCAACACCCGACAACCTTCCCTCGTGACGAGACGCTGGAACTCCGATATGATCGGCATCAGACATGTAATTAAC
Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 21.10% | 16.70% | 26.83% | 35.38% | NA |
All Indica | 2759 | 4.20% | 0.60% | 37.55% | 57.67% | NA |
All Japonica | 1512 | 49.50% | 49.70% | 0.20% | 0.66% | NA |
Aus | 269 | 1.50% | 0.40% | 79.18% | 18.96% | NA |
Indica I | 595 | 7.60% | 0.20% | 30.25% | 62.02% | NA |
Indica II | 465 | 3.40% | 1.50% | 24.95% | 70.11% | NA |
Indica III | 913 | 1.50% | 0.20% | 50.49% | 47.75% | NA |
Indica Intermediate | 786 | 5.20% | 0.80% | 35.50% | 58.52% | NA |
Temperate Japonica | 767 | 72.90% | 26.50% | 0.39% | 0.26% | NA |
Tropical Japonica | 504 | 12.30% | 86.70% | 0.00% | 0.99% | NA |
Japonica Intermediate | 241 | 52.70% | 46.10% | 0.00% | 1.24% | NA |
VI/Aromatic | 96 | 97.90% | 0.00% | 2.08% | 0.00% | NA |
Intermediate | 90 | 36.70% | 25.60% | 15.56% | 22.22% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg1014304342 | C -> A | LOC_Os10g27140.1 | missense_variant ; p.Pro744His; MODERATE | nonsynonymous_codon ; P744H | Average:13.001; most accessible tissue: Callus, score: 25.315 | probably damaging | 3.284 | DELETERIOUS | 0.02 |
vg1014304342 | C -> DEL | LOC_Os10g27140.1 | N | frameshift_variant | Average:13.001; most accessible tissue: Callus, score: 25.315 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1014304342 | NA | 9.81E-07 | mr1129 | 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 |
vg1014304342 | NA | 9.18E-09 | mr1668 | 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 |
vg1014304342 | NA | 2.33E-11 | mr1864 | 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 |
vg1014304342 | NA | 9.96E-11 | mr1668_2 | 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 |