DOI: 10.5061/dryad.cv4r7
title: Data from: Entire plastid phylogeny of the carrot genus (Daucus, Apiaceae): Concordance with nuclear data and mitochondrial and nuclear DNA insertions to the plastid

description: PREMISE OF THE STUDY: We explored the phylogenetic utility of entire
 plastid DNA sequences in Daucus and compared the results with prior
 phylogenetic results using plastid and nuclear DNA sequences. METHODS: We
 used Illumina sequencing to obtain full plastid sequences of 37 accessions
 of 20 Daucus taxa and outgroups, analyzed the data with phylogenetic
 methods, and examined evidence for mitochondrial DNA transfer to the
 plastid (DcMP). KEY RESULTS: Our phylogenetic trees of the entire data set
 were highly resolved, with 100% bootstrap support for most of the external
 and many of the internal clades, except for the clade of D. carota and its
 most closely related species D. syrticus. Subsets of the data, including
 regions traditionally used as phylogenetically informative regions,
 provide various degrees of soft congruence with the entire data set. There
 are areas of hard incongruence, however, with phylogenies using nuclear
 data. We extended knowledge of a mitochondrial to plastid DNA insertion
 sequence previously named DcMP and identified the first instance in
 flowering plants of a sequence of potential nuclear genome origin inserted
 into the plastid genome. There is a relationship of inverted repeat
 junction classes and repeat DNA to phylogeny, but no such relationship
 with nonsynonymous mutations. CONCLUSIONS: Our data have allowed us to (1)
 produce a well-resolved plastid phylogeny of Daucus, (2) evaluate subsets
 of the entire plastid data for phylogeny, (3) examine evidence for plastid
 and nuclear DNA phylogenetic incongruence, and (4) examine mitochondrial
 and nuclear DNA insertion into the plastid.
description: Daucus_plastid_referencesFasta files of plastid reference sequences. These references contains only 1 inverted repeat. The full sequences have been submitted to GenBank (KX832299-KX832335).Caucalis_platycarpos_649446Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat. Commands used to create bam file is as follows: bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam samtools view -bt reference.fa.fai -o name.bam name.sam samtools sort name.bam name.s samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam samtools index name.sq.bam java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam bwa version 0.7.15-r1140 samtools version 0.1.19-44428cd java version 1.8.0_111 picard version 2.7.1Daucus_aureus_319403Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat. Commands used to create bam file is as follows: bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam samtools view -bt reference.fa.fai -o name.bam name.sam samtools sort name.bam name.s samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam samtools index name.sq.bam java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam bwa version 0.7.15-r1140 samtools version 0.1.19-44428cd java version 1.8.0_111 picard version 2.7.1Daucus_bicolor_652321Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat. Commands used to create bam file is as follows: bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam samtools view -bt reference.fa.fai -o name.bam name.sam samtools sort name.bam name.s samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam samtools index name.sq.bam java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam bwa version 0.7.15-r1140 samtools version 0.1.19-44428cd java version 1.8.0_111 picard version 2.7.1Daucus_bicolor_Ames_25830Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat. Commands used to create bam file is as follows: bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam samtools view -bt reference.fa.fai -o name.bam name.sam samtools sort name.bam name.s samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam samtools index name.sq.bam java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam bwa version 0.7.15-r1140 samtools version 0.1.19-44428cd java version 1.8.0_111 picard version 2.7.1Daucus_carota_subsp._capillifolius_279764Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat. Commands used to create bam file is as follows: bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam samtools view -bt reference.fa.fai -o name.bam name.sam samtools sort name.bam name.s samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam samtools index name.sq.bam java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam bwa version 0.7.15-r1140 samtools version 0.1.19-44428cd java version 1.8.0_111 picard version 2.7.1Daucus_carota_subsp._carota_274297Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat. Commands used to create bam file is as follows: bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam samtools view -bt reference.fa.fai -o name.bam name.sam samtools sort name.bam name.s samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam samtools index name.sq.bam java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam bwa version 0.7.15-r1140 samtools version 0.1.19-44428cd java version 1.8.0_111 picard version 2.7.1Daucus_carota_subsp._carota_502244Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat. Commands used to create bam file is as follows: bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam samtools view -bt reference.fa.fai -o name.bam name.sam samtools sort name.bam name.s samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam samtools index name.sq.bam java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam bwa version 0.7.15-r1140 samtools version 0.1.19-44428cd java version 1.8.0_111 picard version 2.7.1Daucus_carota_subsp._carota_652393Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat. Commands used to create bam file is as follows: bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam samtools view -bt reference.fa.fai -o name.bam name.sam samtools sort name.bam name.s samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam samtools index name.sq.bam java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam bwa version 0.7.15-r1140 samtools version 0.1.19-44428cd java version 1.8.0_111 picard version 2.7.1Daucus_carota_subsp._carota_Ames_27395Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat. Commands used to create bam file is as follows: bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam samtools view -bt reference.fa.fai -o name.bam name.sam samtools sort name.bam name.s samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam samtools index name.sq.bam java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam bwa version 0.7.15-r1140 samtools version 0.1.19-44428cd java version 1.8.0_111 picard version 2.7.1Daucus_carota_subsp._gummifer_478883Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat. Commands used to create bam file is as follows: bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam samtools view -bt reference.fa.fai -o name.bam name.sam samtools sort name.bam name.s samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam samtools index name.sq.bam java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam bwa version 0.7.15-r1140 samtools version 0.1.19-44428cd java version 1.8.0_111 picard version 2.7.1Daucus_carota_subsp._gummifer_Ames_26381Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat. Commands used to create bam file is as follows: bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam samtools view -bt reference.fa.fai -o name.bam name.sam samtools sort name.bam name.s samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam samtools index name.sq.bam java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam bwa version 0.7.15-r1140 samtools version 0.1.19-44428cd java version 1.8.0_111 picard version 2.7.1Daucus_carota_subsp._gummifer_Ames_26383Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat. Commands used to create bam file is as follows: bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam samtools view -bt reference.fa.fai -o name.bam name.sam samtools sort name.bam name.s samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam samtools index name.sq.bam java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam bwa version 0.7.15-r1140 samtools version 0.1.19-44428cd java version 1.8.0_111 picard version 2.7.1Daucus_carota_subsp._gummifer_Ames_31194Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat. Commands used to create bam file is as follows: bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam samtools view -bt reference.fa.fai -o name.bam name.sam samtools sort name.bam name.s samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam samtools index name.sq.bam java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam bwa version 0.7.15-r1140 samtools version 0.1.19-44428cd java version 1.8.0_111 picard version 2.7.1Daucus_carota_subsp._maximus_Ames_26408Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat. Commands used to create bam file is as follows: bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam samtools view -bt reference.fa.fai -o name.bam name.sam samtools sort name.bam name.s samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam samtools index name.sq.bam java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam bwa version 0.7.15-r1140 samtools version 0.1.19-44428cd java version 1.8.0_111 picard version 2.7.1Daucus_conchitae_652367Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat. Commands used to create bam file is as follows: bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam samtools view -bt reference.fa.fai -o name.bam name.sam samtools sort name.bam name.s samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam samtools index name.sq.bam java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam bwa version 0.7.15-r1140 samtools version 0.1.19-44428cd java version 1.8.0_111 picard version 2.7.1Daucus_conchitae_652375Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat. Commands used to create bam file is as follows: bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam samtools view -bt reference.fa.fai -o name.bam name.sam samtools sort name.bam name.s samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam samtools index name.sq.bam java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam bwa version 0.7.15-r1140 samtools version 0.1.19-44428cd java version 1.8.0_111 picard version 2.7.1Daucus_conchitae_652385Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat. Commands used to create bam file is as follows: bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam samtools view -bt reference.fa.fai -o name.bam name.sam samtools sort name.bam name.s samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam samtools index name.sq.bam java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam bwa version 0.7.15-r1140 samtools version 0.1.19-44428cd java version 1.8.0_111 picard version 2.7.1Daucus_crinitus_652412Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat. Commands used to create bam file is as follows: bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam samtools view -bt reference.fa.fai -o name.bam name.sam samtools sort name.bam name.s samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam samtools index name.sq.bam java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam bwa version 0.7.15-r1140 samtools version 0.1.19-44428cd java version 1.8.0_111 picard version 2.7.1Daucus_crinitus_652413Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat. Commands used to create bam file is as follows: bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam samtools view -bt reference.fa.fai -o name.bam name.sam samtools sort name.bam name.s samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam samtools index name.sq.bam java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam bwa version 0.7.15-r1140 samtools version 0.1.19-44428cd java version 1.8.0_111 picard version 2.7.1Daucus_glochidiatus_285038Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat. Commands used to create bam file is as follows: bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam samtools view -bt reference.fa.fai -o name.bam name.sam samtools sort name.bam name.s samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam samtools index name.sq.bam java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam bwa version 0.7.15-r1140 samtools version 0.1.19-44428cd java version 1.8.0_111 picard version 2.7.1Daucus_guttatus_286611Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat. Commands used to create bam file is as follows: bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam samtools view -bt reference.fa.fai -o name.bam name.sam samtools sort name.bam name.s samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam samtools index name.sq.bam java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam bwa version 0.7.15-r1140 samtools version 0.1.19-44428cd java version 1.8.0_111 picard version 2.7.1Daucus_guttatus_652233Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat. Commands used to create bam file is as follows: bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam samtools view -bt reference.fa.fai -o name.bam name.sam samtools sort name.bam name.s samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam samtools index name.sq.bam java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam bwa version 0.7.15-r1140 samtools version 0.1.19-44428cd java version 1.8.0_111 picard version 2.7.1Daucus_involucratus_652332Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat. Commands used to create bam file is as follows: bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam samtools view -bt reference.fa.fai -o name.bam name.sam samtools sort name.bam name.s samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam samtools index name.sq.bam java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam bwa version 0.7.15-r1140 samtools version 0.1.19-44428cd java version 1.8.0_111 picard version 2.7.1Daucus_involucratus_652350Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat. Commands used to create bam file is as follows: bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam samtools view -bt reference.fa.fai -o name.bam name.sam samtools sort name.bam name.s samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam samtools index name.sq.bam java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam bwa version 0.7.15-r1140 samtools version 0.1.19-44428cd java version 1.8.0_111 picard version 2.7.1Daucus_littoralis_295857Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat. Commands used to create bam file is as follows: bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam samtools view -bt reference.fa.fai -o name.bam name.sam samtools sort name.bam name.s samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam samtools index name.sq.bam java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam bwa version 0.7.15-r1140 samtools version 0.1.19-44428cd java version 1.8.0_111 picard version 2.7.1Daucus_muricatus_295863Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat. Commands used to create bam file is as follows: bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam samtools view -bt reference.fa.fai -o name.bam name.sam samtools sort name.bam name.s samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam samtools index name.sq.bam java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam bwa version 0.7.15-r1140 samtools version 0.1.19-44428cd java version 1.8.0_111 picard version 2.7.1Daucus_muricatus_Ames_29090Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat. Commands used to create bam file is as follows: bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam samtools view -bt reference.fa.fai -o name.bam name.sam samtools sort name.bam name.s samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam samtools index name.sq.bam java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam bwa version 0.7.15-r1140 samtools version 0.1.19-44428cd java version 1.8.0_111 picard version 2.7.1Daucus_pusillus_349267Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat. Commands used to create bam file is as follows: bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam samtools view -bt reference.fa.fai -o name.bam name.sam samtools sort name.bam name.s samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam samtools index name.sq.bam java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam bwa version 0.7.15-r1140 samtools version 0.1.19-44428cd java version 1.8.0_111 picard version 2.7.1Daucus_pusillus_661242Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat. Commands used to create bam file is as follows: bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam samtools view -bt reference.fa.fai -o name.bam name.sam samtools sort name.bam name.s samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam samtools index name.sq.bam java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam bwa version 0.7.15-r1140 samtools version 0.1.19-44428cd java version 1.8.0_111 picard version 2.7.1Daucus_setulosus_652329Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat. Commands used to create bam file is as follows: bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam samtools view -bt reference.fa.fai -o name.bam name.sam samtools sort name.bam name.s samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam samtools index name.sq.bam java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam bwa version 0.7.15-r1140 samtools version 0.1.19-44428cd java version 1.8.0_111 picard version 2.7.1Daucus_setulosus_652360Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat. Commands used to create bam file is as follows: bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam samtools view -bt reference.fa.fai -o name.bam name.sam samtools sort name.bam name.s samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam samtools index name.sq.bam java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam bwa version 0.7.15-r1140 samtools version 0.1.19-44428cd java version 1.8.0_111 picard version 2.7.1Daucus_syrticus_Ames_29096Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat. Commands used to create bam file is as follows: bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam samtools view -bt reference.fa.fai -o name.bam name.sam samtools sort name.bam name.s samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam samtools index name.sq.bam java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam bwa version 0.7.15-r1140 samtools version 0.1.19-44428cd java version 1.8.0_111 picard version 2.7.1Daucus_syrticus_Ames_29108Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat. Commands used to create bam file is as follows: bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam samtools view -bt reference.fa.fai -o name.bam name.sam samtools sort name.bam name.s samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam samtools index name.sq.bam java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam bwa version 0.7.15-r1140 samtools version 0.1.19-44428cd java version 1.8.0_111 picard version 2.7.1Daucus_tenuisectus_Ames_31616Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat. Commands used to create bam file is as follows: bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam samtools view -bt reference.fa.fai -o name.bam name.sam samtools sort name.bam name.s samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam samtools index name.sq.bam java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam bwa version 0.7.15-r1140 samtools version 0.1.19-44428cd java version 1.8.0_111 picard version 2.7.1Oenanthe_virgata_Ames_30293Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat. Commands used to create bam file is as follows: bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam samtools view -bt reference.fa.fai -o name.bam name.sam samtools sort name.bam name.s samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam samtools index name.sq.bam java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam bwa version 0.7.15-r1140 samtools version 0.1.19-44428cd java version 1.8.0_111 picard version 2.7.1Pseudorlaya_pumila_662301Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat. Commands used to create bam file is as follows: bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam samtools view -bt reference.fa.fai -o name.bam name.sam samtools sort name.bam name.s samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam samtools index name.sq.bam java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam bwa version 0.7.15-r1140 samtools version 0.1.19-44428cd java version 1.8.0_111 picard version 2.7.1Rouya_polygama_674284Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat. Commands used to create bam file is as follows: bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam samtools view -bt reference.fa.fai -o name.bam name.sam samtools sort name.bam name.s samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam samtools index name.sq.bam java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam bwa version 0.7.15-r1140 samtools version 0.1.19-44428cd java version 1.8.0_111 picard version 2.7.1