The Woman and the Dragon. Exposition of Rev 12 in Christian Traditions

This work deals with the text of the twelfth chapter of Revelation of John. Powered by TCPDF (www.tcpdf.org

hisD reads aligned to native genome (top) and heterologous genome (bottom).

<p>Substantial read loss due to high-density SNP clusters can be seen in the non-native reference.</p

Log-fold changes of read counts for all <i>E</i>. <i>coli</i> strain K12 genes as aligned to both native and heterologous references.

<p>The same read sets as aligned to both reference genomes reveals the extent of bias present due to differences in the choice of reference genome.</p

Structural differences between reference strains for <i>E</i>. <i>coli</i> (left) and V. Vulnificus (right).

<p>A 2.64% difference is observed between references in <i>E</i>. <i>coli</i> and a 3.61% difference is observed in <i>V</i>. <i>Vulnificus</i>, accounting for indels and polymorphic sites.</p

Operon structure containing the gene, cusC, which is responsible for copper resistance in <i>E</i>. <i>coli</i>.

<p>21 SNPs are present across 1373 bases between the K12 and IAI1 reference strains.</p

Simulation of the relationship between SNPs and read length shown using bowtie2’s—Very-sensitive alignment settings.

<p>Modest reduction in bias was observed in these simulations with regard to standard alignment parameters.</p

Log-fold differences in native vs heterologous alignment for different read lengths.

<p>Shorter reads handle mapping more poorly and are subject to significant bias in non-native alignments, while bias is minimalized with increasing read length.</p

Data processing pipeline.

<p>Orthology is identified between heterologous strains and reads are aligned to both reference genomes. Using the orthology mapping information, extrapolated read alignment counts are compiled such that counts can be compared for each read set as aligned to each reference genome.</p

Simulation of the relationship between SNPs and read length with each gene containing 35 randomly distributed SNPs and simulated reads of length 50, 100, and 150.

<p>Log-fold changes in read alignment for native and heterologous genomes show that shorter reads perform poorly when aligned to heterologous genomes, while longer reads are more resilient.</p

Summary of read data, including average coverage when reads are mapped to native or heterologous genomes.

<p>Summary of read data, including average coverage when reads are mapped to native or heterologous genomes.</p