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The discrepancy of about 5% could be explained by missing sequence data from centromeric regions.
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We impute the missing sequence data by replacing it with its closest neighbor with respect to sequence similarity from among the complete allele sequences.
Whenever possible, therefore, we compensated for missing sequence data by including in our analyses 28S rDNA sequences for other representatives of the same genera.
An "N/A" not available indicates missing sequence data.
Haplotyping can aid the detection and correction of erroneous or missing sequencing data - for example, by detecting inconsistencies between the genotypes within a family [ 8, 64 ].
Notably, both the current study and [ 44] used the same Bayesian analytical framework which ensures that missing data will not lead to high FST, because it fully accounts for uncertainty in genotypes, allele frequencies, and FST caused by missing data and low sequence coverage.
Missing sequences for certain taxa in certain partitions were coded as missing data in the respective alignments.
Since all the sequences are affected by missing data, one must extrapolate the entropy rate from missing data to full data.
To avoid biases introduced by missing data from the published sequences, we used a fragment (corresponding to ca. 95% of SSU rRNA) spanning from helix 5 until 2 bp before helix 50 (i.e. positions 48 1896 in Amphimedon queenslandica), and only considered the 123 sequences without data missing within this region (listed in Additional file 4).
Sensitivity analyses in both studies, including a LOCF approach, and comparison of characteristics of patients with and without baseline FSS data in the PILLAR study (Table 3), indicated that the FSS results were unaffected by missing data.> -wrap-foot> †Median; ‡NS5B sequence-based assay.
The study was affected by missing data.
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