pero_in.454.fasta

This file contains 454 generated fastq reads for the Peromyscus samples used for the probe development. Both individuals included in the concatenated reference sequence are within this file, with USNM 569292 represented as 92. Sample USNM 569298 is represented as reads ID'd as 98

chimera_ID

This script sorts capture sequences that hit to non-closest-relative (NCR) MMA probes

WMG_Alignment26Ind_FINAL01.09.14

All mitochondrial genomes used for array design. 16 are published sequences and 10 are novel mitogenomes

combiner-2.0

The FASTA file is sequences from MMA capture. The Blast output is the output of blasting those sequences against the MMA probeset, minus closest relative to the target species (non-closest-relative, or NCR, probeset). This program appends the length of the query sequence (found in the FASTA file) onto the end of that sequence's line in the blast table so that the chimera detection decision rules can be followed in chimera_ID.p

H3FTPWM01

454 Sequencing reads for some of newly generated mitogenomes, a text file is provided with demultiplexing information and for this run

H3HWW5Q01

Second 454 run containing novel mitogenomes. Details for demultiplexing are provided in a separate text file

sequenceGetter-4.0

This script gets a subset of a FASTA file based on a CSV file of BLAST hits

Enrichment Assemblies

These are all 63 assemblies, in bam format with the resulting consensus sequences as fasta. All sequences are labelled by capture pool ID in table 2

AllProbes_good

This file contains all 8,178 probes used for RNA bait synthesis

Nonsynonymous and Synonymous Substitutions.

<p>Nonsynonymous and Synonymous Substitutions.</p