MOESM1 of AdapterRemoval v2: rapid adapter trimming, identification, and read merging

Additional File 1: Table S1. Adapter-trimming and read-merging performance. Tabular representation of performance metrics for trimming of single adapter-pairs, multiple adapter-pairs, and merging of overlapping read pairs (Fig. 1)

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

Image1_Identification of genetic variants associated with a wide spectrum of phenotypes clinically diagnosed as Sanfilippo and Morquio syndromes using whole genome sequencing.jpeg

Mucopolysaccharidoses (MPSs) are inherited lysosomal storage disorders (LSDs). MPSs are caused by excessive accumulation of mucopolysaccharides due to missing or deficiency of enzymes required for the degradation of specific macromolecules. MPS I-IV, MPS VI, MPS VII, and MPS IX are sub-types of mucopolysaccharidoses. Among these, MPS III (also known as Sanfilippo) and MPS IV (Morquio) syndromes are lethal and prevalent sub-types. This study aimed to identify causal genetic variants in cases of MPS III and MPS IV and characterize genotype-phenotype relations in Pakistan. We performed clinical, biochemical and genetic analysis using Whole Genome Sequencing (WGS) in 14 Pakistani families affected with MPS III or MPS IV. Patients were classified into MPS III by history of aggressive behaviors, dementia, clear cornea and into MPS IV by short trunk, short stature, reversed ratio of upper segment to lower segment with a short upper segment. Data analysis and variant selections were made based on segregation analysis, examination of known MPS III and MPS IV genes, gene function, gene expression, the pathogenicity of variants based on ACMG guidelines and in silico analysis. In total, 58 individuals from 14 families were included in the present study. Six families were clinically diagnosed with MPS III and eight families with MPS IV. WGS revealed variants in MPS-associated genes including NAGLU, SGSH, GALNS, GNPTG as well as the genes VWA3B, BTD, and GNPTG which have not previously associated with MPS. One family had causal variants in both GALNS and BTD. Accurate and early diagnosis of MPS in children represents a helpful step for designing therapeutic strategies to protect different organs from permanent damage. In addition, pre-natal screening and identification of genetic etiology will facilitate genetic counselling of the affected families. Identification of novel causal MPS genes might help identifying new targeted therapies to treat LSDs.</p

Image2_Identification of genetic variants associated with a wide spectrum of phenotypes clinically diagnosed as Sanfilippo and Morquio syndromes using whole genome sequencing.jpeg

Mucopolysaccharidoses (MPSs) are inherited lysosomal storage disorders (LSDs). MPSs are caused by excessive accumulation of mucopolysaccharides due to missing or deficiency of enzymes required for the degradation of specific macromolecules. MPS I-IV, MPS VI, MPS VII, and MPS IX are sub-types of mucopolysaccharidoses. Among these, MPS III (also known as Sanfilippo) and MPS IV (Morquio) syndromes are lethal and prevalent sub-types. This study aimed to identify causal genetic variants in cases of MPS III and MPS IV and characterize genotype-phenotype relations in Pakistan. We performed clinical, biochemical and genetic analysis using Whole Genome Sequencing (WGS) in 14 Pakistani families affected with MPS III or MPS IV. Patients were classified into MPS III by history of aggressive behaviors, dementia, clear cornea and into MPS IV by short trunk, short stature, reversed ratio of upper segment to lower segment with a short upper segment. Data analysis and variant selections were made based on segregation analysis, examination of known MPS III and MPS IV genes, gene function, gene expression, the pathogenicity of variants based on ACMG guidelines and in silico analysis. In total, 58 individuals from 14 families were included in the present study. Six families were clinically diagnosed with MPS III and eight families with MPS IV. WGS revealed variants in MPS-associated genes including NAGLU, SGSH, GALNS, GNPTG as well as the genes VWA3B, BTD, and GNPTG which have not previously associated with MPS. One family had causal variants in both GALNS and BTD. Accurate and early diagnosis of MPS in children represents a helpful step for designing therapeutic strategies to protect different organs from permanent damage. In addition, pre-natal screening and identification of genetic etiology will facilitate genetic counselling of the affected families. Identification of novel causal MPS genes might help identifying new targeted therapies to treat LSDs.</p

structure file Genome-wide SNP catalogue in Lagenorhynchus spp

Tab Separated Values File in "Structure" format. This file was used to run the software "Admixture". Missing data=0, A=1, C=2, G=3, T=4

Probability, random processes, and ergodic properties

In this new edition of this classic text, much of the material has been rearranged and revised for pedagogical reasons. Many classic inequalities and proofs are now incorporated into the text, and many citations have been added

Additional file 11: Figure S3. of Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds

MNEc2M Inter-SNP distance and informativeness by breed. Distance between SNPs on the MNEc2M array were calculated by breed group (See Additional file 5: Table S5) at various minor allele frequency cutoffs (0, 0.01, 0.03, 0.05, 0.10). Breed groups with asterisk (*) indicate a combination of studbook breeds. (PNG 1152 kb