Briefly, we used an in-house pipeline for statistic sequencing error rates, base calling accuracy and ATCG base contents of raw sequencing data.
We used the ρ statistic (mean sequence divergence from the inferred ancestral haplotype of the clade in question) with a mutation rate estimate for the complete mtDNA sequence of one transition in every 3,624 years [ 31], correcting for purifying selection by using the calculator provided with that paper.
Sliding window approaches have often been used to find clustered values of some statistic along a sequence [see e.g. [ 63, 81]], but this approach has some drawbacks.
The enrichment results are validated by the 'mixed' sequencing statistic, which indicates the fraction of beads in the run that give signals indicating a likelihood that the attached DNA molecules are of nonuniform sequence.
Much of the discussion centers around the DNA-sequence statistic S, which is defined as the sum of the square-frequencies of the letters: S = (f_a)^2, + (f_c)^2 + (f_g)^2 + (f_t)^2 where f_a, f_c, f_g, and f_t are the base frequencies.
The haplotype frequency-based statistics are more sensitive for small sample sizes, while the sequence based statistic is a more sensitive method for detecting population structure in highly polymorphic loci [25], (see Text S1 for specific examples).
Tajima's D statistic for full-length sequence alignment was −2.806 (Table 2), demonstrating a weak purifying selection during the evolutionary process of A(H1N1 pdm in 2009.
The statistic numbers associated to sequence data processing are shown in Table 1.
The only CagA protein could not provide any statistic information about its sequence features as a T4S effector either.
The gene coding for the GABA transporter, slc6a11, was significantly down-regulated in fluoxetine treated fish with RNA-sequencing (test statistic = 6.06, p = 4.49 × 10-7, Figure 3A).
