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Before conducting further analysis, we checked assembly data of BAC contig, and found no apparent errors (data not shown).
We amplified and sequenced the regions that contained indels to confirm that such features were not caused by sequencing errors (data not shown).
Similarly, multilevel modeling including random water zone effects had negligible impact on the regression coefficients and their standard errors (data not shown).
SYCP3 was first detectable in leptotene-stage spermatocytes of both Bscl2+/+ and Bscl2−/− preparations and progressively labeled the axial extension of the condensing chromosomes during zygotene and pachytene stages without indication for chromosome pairing errors (data not shown).
Read mapping was used to confirm that the observed absence of S. Virchow SL491 prophage and islands regions in S. Virchow SVQ1 was genuine and not as the result of assembly errors (data not shown).
(At suggested nucleotide substitution rate of 3 × 10-4 and insertion/deletion error rates of approximately 2 × 10-4 (Tarjei Mikkelsen, personal communication) we expect few if any of these disruptions to arise from sequencing errors (data not shown)).
Similar(52)
Additional salts, i.e., NaBr and NaNO3, exhibited almost identical profiles, within experimental error (data not shown).
In all of the samples tested, the results of the Sequenome method matched those from restriction digests, suggesting that the lack of detection of -61CC homozygotes was not due to methodological error (data not shown).
A similar analysis indicated that, overall, substitution rates are relatively unaffected by sequencing error (data not shown), but that error can inflate the ratio of nonsynonymous to synonymous substitution rates (dN/dS) in protein-coding genes by as much as ∼10% (Methods S2 and Table S3).
For PsTRXh2, the [U]50% of both denaturation curves (followed by CD and fluorescence) are well-resolved (see Results) and the above equation can be applied, but we also carried out a three-state analysis of the GdmCl-denaturation data leading to a result similar to the two-state model, within the experimental error (data not shown) (see [35] for a discussion).
This procedure had little impact on the error in estimating differences between pools, with no change in the mean error (data not shown).
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