A threshold of 9 or more total sequences for each gene was selected to be applied for our dataset, to be able to include only the most reliable data for analysis.
Despite CAP3 employing a higher stringency as compared to PHRAP [ 66], PHRAP assemblies of both BAC clones resulted in fewer but higher quality contigs which included more total sequences (PGB02: contigs contigs, PHRAP 14 contigs; PGB04: contigs contigs, PHRAP 14 contigs).
For example, our threespine stickleback maps presented here are larger in total genetic distance than those in the work by Roesti et al. (2013); however, we analyzed more than twice as many F2 fish, sequenced paired end reads vs. single end reads, and generated more total sequences than in this previous study.
In more than 90% of bacterial genomes the coding sequence makes up 80% or more of total sequence (mean 86%) (Figure 2).
For SSRs whose unit sequence is two or more nucleotides, the total sequence of the reported SSR is the largest possible one, including overlapping repeated patterns.
In some species, e.g. H. kukui, H. setosifrons, and some populations of H. connectens, polymorphic sites in heteroplasmic individuals accounted for 5-65-6% mofe of the total sequence (Fig. 1).
Whereas approximately equal numbers of abundant OTUs (defined by more than 1% total sequence abundance) increased towards either the vent or control site, more OTUs of intermediate abundance level (defined by more than two sequence occurrences, but less than 1% total sequence abundance) tended to increase towards the vent site than towards the control site (Table S4).
The gypsy family of long terminal repeat (LTR) retrotransposable elements were by far the most abundant type of class I-TE, with 71 out of the 86 transposons found (51 of which were complete with intact TSDs) and occupying more than half the total sequence of ctg1034 (51.24%).
To reduce noise and eliminate highly conserved sites that provide little information about covariation, we considered only sites with no gaps [ 52] and the most frequent residue occupying no more than half of the total sequence weights.
MALDI-TOF/TOF MS identified full-length mature human ApoAI (P02647) with total sequence coverage more than 90%, as indicated by the identified peptides shown in Table S2 in Additional file 3. Western blotting for ApoAI showed no significant difference in band intensity between four BC and four HV samples (data not shown).
