This picture can then be fed into various algorithms such as maximum-likelihood phylogeny [20], [21], [26] in order to reconstruct the evolutionary relationships between the individual sequences.
Variation was highly correlated between the individual sequenced at high coverage and the additional 10 individuals (Spearman's r ranging from 0.53 to 0.68, df = 15,786, p < < 0.001, Figure 1).
Connections between the individual sequences matching bovine markers and human sequence were then determined via BLASTN [ 39] with an expectation value of e-20, and default values for other parameters.
This is because the observed differences not only reflect sequencing errors, which are expected to occur at similar rates across species, but they also reflect true genomic differences between the individuals sequenced for the 2× and ENCODE projects, which will depend on the diversity of the sampled populations, the relatedness of the sampled individuals, and other factors.
In addition, the identity between the two LTRs present in the individual sequences was calculated and appeared to be very high for some of the LTR members (averages of 99.81; 99.64, and 99.83% for Pao-Bel, Copia, and Gypsy, respectively) (Additional File 3).
Taking into account that for some taxa a few short fragments are missing, the alignments of the non-coding intron regions are 387 bp for GAPDH (the individual sequences ranged between 247-269 bp), and 685 bp for ODC (ranging between 577-619 bp for all taxa, except Corvus that, due to a large deletion, is only 429 bp).
These parameters and variable amounts of sequence overlap between the individual consensus sequences within contigs resulted in differential numbers of alignments for overall diversity estimates.
Errors were defined as base pair inconsistencies between an individual sequence and the most common base pair found in that position in the alignment of all sequences.
Variable and informative indels produced the discrepancies between the complete alignment and individual sequence length ranges.
The alignment between the consensus and any individual sequence shows that divergence varies greatly, in nature, position and number (from no divergence for the P. troglodytes SP to 8 differences for O. cuniculus).
