Variant ID: vg0623214938 (JBrowse) | Variation Type: SNP |
Chromosome: chr06 | Position: 23214938 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.03, others allele: 0.00, population size: 126. )
TTAGTGACTCACTACGTTGGTTGCTGCGCATACCCAACAAGTATTTCCCATCTGTATAGGCAGCTGCCCACTTCTCCCTTAGTCGGTACATCGATCAGGG[C/T]
GATCCATTGACCATTCCCCGTGCCTCCATTCTCCTTAAAATCAGCCCAACGTCTCTCGAACTCCTCCTCATCCATACTCTTATAAATTAATTTTCTTAGC
GCTAAGAAAATTAATTTATAAGAGTATGGATGAGGAGGAGTTCGAGAGACGTTGGGCTGATTTTAAGGAGAATGGAGGCACGGGGAATGGTCAATGGATC[G/A]
CCCTGATCGATGTACCGACTAAGGGAGAAGTGGGCAGCTGCCTATACAGATGGGAAATACTTGTTGGGTATGCGCAGCAACCAACGTAGTGAGTCACTAA
Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 87.60% | 12.30% | 0.06% | 0.00% | NA |
All Indica | 2759 | 85.50% | 14.40% | 0.11% | 0.00% | NA |
All Japonica | 1512 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
Aus | 269 | 37.90% | 62.10% | 0.00% | 0.00% | NA |
Indica I | 595 | 97.30% | 2.70% | 0.00% | 0.00% | NA |
Indica II | 465 | 88.40% | 11.60% | 0.00% | 0.00% | NA |
Indica III | 913 | 78.10% | 21.70% | 0.22% | 0.00% | NA |
Indica Intermediate | 786 | 83.50% | 16.40% | 0.13% | 0.00% | NA |
Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 91.70% | 8.30% | 0.00% | 0.00% | NA |
Intermediate | 90 | 93.30% | 6.70% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0623214938 | C -> T | LOC_Os06g39090.1 | missense_variant ; p.Ala270Thr; MODERATE | nonsynonymous_codon ; A270I | Average:54.53; most accessible tissue: Minghui63 young leaf, score: 80.562 | possibly damaging | 1.935 | TOLERATED | 0.06 |
vg0623214938 | C -> T | LOC_Os06g39090.1 | missense_variant ; p.Ala270Thr; MODERATE | nonsynonymous_codon ; A270T | Average:54.53; most accessible tissue: Minghui63 young leaf, score: 80.562 | possibly damaging | 1.571 | TOLERATED | 0.67 |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0623214938 | NA | 8.10E-06 | mr1004 | 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 |
vg0623214938 | 2.12E-06 | 2.96E-06 | mr1012 | 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 |