Base composition bias: AT <i>versus</i> BE libraries.

<p>Fresh aliquots of <i>E. coli</i> DNA extracts were sheared using the Covaris E210 sonicator, size selected, and built into AT and BE libraries (adapter concentration  =  0.6 µM). We report the base composition observed at the first 10 (positions 1 to 10) and last 10 (positions N-9 to N) nucleotide positions within sequence reads mapping with high quality a unique position of the <i>E. coli</i> NC_010473 genome. The genomic composition of the 10 nucleotides located upstream (positions –10 to –1) and downstream (positions N+1 to N+10) DNA inserts are also provided.</p

Nucleotide misincorporation bias for ancient DNA templates: AT <i>versus</i> BE libraries.

<p>Aliquots of a quagga museum specimen and an <i>Hippidion</i> bone fossil were built into AT and BE libraries. We report CT mismatch rates at the first 5 (positions 1 to 5) and last 5 (positions –1 to –5) nucleotide positions within sequence reads mapping with high quality a unique position of the EquCab2.0 genome. These rates are calculated using mapDamage output <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078575#pone.0078575-Ginolhac1" target="_blank">[24]</a> by summing over positions where a C (G) is found in the reference genome but a T (A) is found in sequencing reads.</p

Base composition bias for ancient DNA templates: AT <i>versus</i> BE libraries.

<p>Aliquots of a quagga museum specimen and an <i>Hippidion</i> bone fossil were built into AT and BE libraries. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078575#pone-0078575-g002" target="_blank">Figure 2</a> captions for further information regarding base compositions.</p

Sequence data.

<p>The number of raw sequence read pairs generated as well as the number of collapsed trimmed reads and the number of unique hits to reference genomes and passing quality filters are indicated. Endogenous DNA content was calculated by dividing the total number of unique hits passing quality filters and the total number of collapsed reads. BE: Blunt-End adapter ligation. AT: AT-overhang adapter ligation. The final concentration of adapter used for ligation is reported as standard (S) or low (L; see Material and Methods). C: Covaris sonication. B: Bioruptor sonication. N: Nebulization. While most DNA libraries were sequenced as Paired-End (2×100 cycles), one, indicated with an asterisk, was sequenced as Single-End. For this DNA library, #Collapsed refers to the numbers of reads considered post-trimming and not post-collapsing, as for other DNA libraries.</p