表紙・目次 : 『千葉医学雑誌』 93巻3号 2017年6月

Exabayes phylogeny based on partitioned, concatenated analysis of 97 UCE loci (corresponding to our 100% complete matrix, with sequences of 55 of 55 taxa present for each locus)

Data-Supporting-FigureS12

Number of Illumina GAIIx reads returned for Epicentre Nextera indexes versus indexes designed using EDITTAG and incorporated to Epicentre Nextera-style sequencing adapters

Data-Supporting-FigureS11

Number of 454 FLX Titanium reads returned for PCR primers incorporating 10 nt edit distance sequence tags and amplifying RbcLa in land plants

Data-Supporting-FigureS13

Number of Illumina GAIIx reads returned for TruSeq-style adapters incorporating indexes designed using EDITTAG and ligated onto pooled DNA templates (Tab 1) versus the number of Illumina HiSeq 2000 reads returned for TruSeq-style adapters incorporating indexes designed using EDITTAG and ligated onto DNA individually. The variance in read number is the important difference to note

Counts of four to 10 nucleotide, ≥3 edit distance sequence tags sets designed using EDITTAG.

<p>We did not include, in any set, sequence tags having >2 homopolymers, GC content outside the range 40%</p

Pairwise edit distance between 25 tags of five nucleotides in length and edit distance three designed using EDITTAG.

<p>Pairwise edit distance between 25 tags of five nucleotides in length and edit distance three designed using EDITTAG.</p

Number of HiSeq reads returned for libraries prepared using Illumina TruSeq adapters versus libraries prepared using adapters integrating edit metric sequence tags designed using EDITTAG.

<p>Number of HiSeq reads returned for libraries prepared using Illumina TruSeq adapters versus libraries prepared using adapters integrating edit metric sequence tags designed using EDITTAG.</p

Commercial and non-commercial sequence tag sets and the conformance of each to the stated or assumed distance metric (edit or Hamming).

1<p>Hamady <i>et al.</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042543#pone.0042543-Hamady1" target="_blank">[31]</a> tags are from the nmeth.1184-S1.pdf supplementary file.</p>2<p>Hamady <i>et al.</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042543#pone.0042543-Hamady1" target="_blank">[31]</a> tags are Hamming distance 4 from one another in binary encoding but Hamming distance 2 from one another in nucleotide encoding.</p>3<p>We generated Meyer <i>et al.</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042543#pone.0042543-Meyer3" target="_blank">[29]</a> tags using: ‘python create_index_sequences.py -l -d 3’.</p>4<p>Adey <i>et al.</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042543#pone.0042543-Adey1" target="_blank">[41]</a> tags are from the gb-2010-11-12-r119-s3.pdf supplementary file.</p>5<p>Meyer <i>et al.</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042543#pone.0042543-Meyer2" target="_blank">[3]</a> tags are from the nprot.2007.520-S1.doc supplementary file.</p>6<p>We generated Frank <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042543#pone.0042543-Frank1" target="_blank">[42]</a> tags using: ‘barcrawl -l -m 3’. BARCRAWL uses a hybrid approach to create distance between tags while accounting for a single deletion.</p><p>This is similar to an expected edit distance of two.</p>7<p>Illumina Nextera tags are incorporated to either end of the template strand in combinatorial fashion to identify up to 96 samples.</p

Insertion and deletion errors violate the codeword scheme and reduce the utility of Hamming-based tags.

<p>Panel (A) shows two sequence tags that are different from one another by seven substitutions (Hamming distance = 7) – a distance more than sufficient to differentiate tags in the presence of substitution errors. However, these same two tags have an edit distance of two (B) – meaning that a total of two insertions, substitutions, or deletions can turn Tag 1 into Tag 2 and confuse samples. Although it seems improbable that two indels or substitutions would occur in a sequence tag, consider the third case (C) in which a single deletion event at the 5′ end of a sequence tag adjoining DNA template beginning with 5′ guanine confuses Tag 1 with Tag 2. Edit metric sequence tags of distance three or greater would mitigate this mistake.</p

wesj-toepads-realigned.bam.placeholder

Merged BAM file that we realigned around indels using GATK. Contains alignment information for all individuals across which we called SNPs using GATK