Fig. 3 Redundancy analysis (RDA) between sequencing result of genus level and environmental factors.
The relationship between sequencing depth and efficacy in the comprehensive detection of SNPs is a key concern from the perspective of cost-effectiveness.
This filter aims to distinguish between sequencing error, which should be found at low frequency, and true polymorphism.
We devised a simple theoretical model to explore the relationship between sequencing error and read coverage as a function of the average coverage.
An appraisal of available analytical methods will better equip researchers to bridge the "next-generation gap" between sequencing and data analysis [10].
Nevertheless, the high correlation in variability estimates between sequencing of pooled individuals and Sanger sequencing indicates that the analysis of pooled samples correctly recovers heterogeneity in variability patterns across the genome.
Focusing analyses on gene-coding regions provides a plausible trade-off between sequencing cost and discovery of informative variants, and may be an attractive study design before genome-wide sequencing study becomes widely available [14], [30], [46], [47], [48].
Correlation between sequencing replicates.
Correlation between sequencing data and antibody titers, following exclusion of subjects with IBD.
Calculation of pairwise correlation coefficients demonstrated a high degree of reproducibility between sequencing runs (Table S1).
Significant discrepancies between sequencing results and PCR fragment sizes were found for markers Ms31 and Ms34.
