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In the family-based Pietrain lines, we found several SNPs in the four regions on SSC2 were significantly associated with scrotal hernia incidence, respectively, after single marker association analysis (Figure 1, Table 1, Table S2).
Minor allele frequencies (MAFs) of the studied polymorphisms were shown in Table 2. Single marker association analysis with a dominant model indicated that SNP rs753529 was significantly associated with BMI in obese subjects (P = 0.026, OR = 0.780, 95% CI = 0.627 0.972).
Single marker association analysis showed a borderline allelic association of the rs6145976 (p = 0.08), rs739669 (p = 0.04), and rs13331 (p = 0.06) with schizophrenia, as summarized in Table S2.
A single marker association analysis revealed that the Kend-L alleles in the QTL region accounted for six to seven additional leaves in long days.
For the case-control study, the single marker association analysis for the genome-wide data was carried out using the 1-df allelic chi-squared test.
Additionally, the T allele at the htSNP 4136 was over represented in control animals in the single marker association analysis (Table 1 and [25]), however, the association was not significant after correcting for the multiple testing.
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The limited power of classical single-marker association analysis for rare variants poses a central challenge in such studies.
Single-marker association analysis [22] and, later, genome-wide association study (GWAS) have been widely used in human genetics [23].
Analyses of the haplotypes were performed using the same linear regression analysis approach as for the single-marker association analysis.
This is alleviated in the LDLA method and LD decay method by the implicit two-marker association analysis.
We performed trait-marker association analysis on the 24 HIFs and found six chromosomal regions which were putatively associated with MRDD resistance.
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