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After gap filling and polishing, the final assembly for W05 is 1013.2 Mb in length, with 988.6 Mb unambiguous bases (Supplementary Figure 1g and Table 1).
We typically used 1/16 the amount of reaction mix, yielding 300 to 400 unambiguous bases.
The mean GC content of the unambiguous bases in the great tit assembly is 40.7%.
GC-content was calculated using a custom Perl script that amalgamated all unique sequences and calculated the proportion of G and C bases in all unambiguous bases.
If this setting were changed to penalize matches to ambiguous bases in the same way as mismatched unambiguous bases, then it would likely reverse the rankings of these two assemblies.
A total of 1,068 unambiguous bases of the cytb gene were sequenced from three mountain tapirs from the Central Andes, Colombia, and 45 lowland tapirs widely sampled across the species distribution range.
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Several unambiguous base-ribose NOE (nuclear Overhauser effect) contacts show that residues C75, C71, and U63 engage in triple interactions with base pairs in the stem G78-C333, G74-C35, and A65-U44, respectovely) to form the caps of the sandwiches.
The identification of the metal ion as a divalent zinc atom was unambiguous based on the electron density maps generated from the multiple anomalous data.
Unambiguous base compositions were derived from the exact mass measurements of the complementary single-stranded oligonucleotides[26]. Quantitative results are obtained by comparing the peak heights with an internal PCR calibration standard present in every PCR well at 100 molecules[20].
The software accept parameters that determine how stringently the nucleotides are discriminated between fully qualified bases (A, C, G, and T), or degenerate bases (using the IUPAC codes) when the intensity files indicate that the probabilities associated with each of the 4 possible nucleotides do not allow an unambiguous base calling.
Direct PCR amplification of ITS yielded single bands and unambiguous base calls, except in C. ficifolia, the sequences of which were therefore not used.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com