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The sequence reads matched to 5517 coding genes in the P. putida KT2440 genome (Nelson et al. 2002), indicating that the sequencing was deep enough to cover almost all kinds of transcripts in the cells.
As the result, approximately 80% of all annotated genes were covered by >70% of their length (Supplementary information file, Figure S1), indicating that the sequencing coverage is sufficient for monitoring low-abundance transcripts.
The SNP allelic frequencies were highly correlated with the percent of abnormal metaphases in 8 del(5q) samples (r = 0.9385, p = 0.0006), indicating that the sequencing data accurately reflects clonality (Figure 2).
From that point, increasing sequence depth results in a slow and stable accumulation of new distinct tags indicating that the sequencing has reached saturation.
Of note, the results from the 7-million-read data were consistent with the conclusions from the whole sequencing data, indicating that the sequencing depth in our study is deep enough.
With an FDR cutoff of 0.01, the consistency percentage dropped to ~ 60% with a genomic coverage of 50, indicating that the sequencing depth indeed affects the detection of RDNP to a large extent.
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Sequencing result indicating that the sequence of irisin was consistent with the modified irisin and the irisin was in frame with α-factor secretion signal ATG.
However, no specific signals were detected in either combination, indicating that the sequence similarity between B. mori and M. sexta is insufficient for cross-hybridization (Fig. S2).
These sequences were not identified in the HGAP2 assembly prior to Quiver-based trimming indicating that the sequences were not erroneously removed during trimming.
There are several N entries upstream of the start codon, indicating that the sequence quality at that site is not good.
The manually validated peptide matches B. abortus 2308 only when the additional nucleotide is removed, indicating that the sequence for locus BAB1_1768 should be corrected.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com