Data from: Entire plastid phylogeny of the carrot genus (Daucus, Apiaceae): Concordance with nuclear data and mitochondrial and nuclear DNA insertions to the plastid

Spooner DM, Ruess H, Iorizzo M, Senalik D, Simon P

Date Published: March 10, 2017

DOI: http://dx.doi.org/10.5061/dryad.cv4r7

 

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Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title Daucus_plastid_references
Downloaded 2 times
Description Fasta files of plastid reference sequences. These references contains only 1 inverted repeat. The full sequences have been submitted to GenBank (KX832299-KX832335).
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Title Caucalis_platycarpos_649446
Downloaded 3 times
Description Bam 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 != "*"' >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 >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
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Title Daucus_aureus_319403
Downloaded 2 times
Description Bam 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 != "*"' >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 >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
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Title Daucus_bicolor_652321
Downloaded 2 times
Description Bam 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 != "*"' >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 >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
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Title Daucus_bicolor_Ames_25830
Downloaded 2 times
Description Bam 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 != "*"' >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 >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
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Title Daucus_carota_subsp._capillifolius_279764
Downloaded 3 times
Description Bam 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 != "*"' >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 >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
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Title Daucus_carota_subsp._carota_274297
Downloaded 2 times
Description Bam 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 != "*"' >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 >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
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Title Daucus_carota_subsp._carota_502244
Downloaded 2 times
Description Bam 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 != "*"' >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 >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
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Title Daucus_carota_subsp._carota_652393
Downloaded 2 times
Description Bam 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 != "*"' >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 >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
Download Daucus_carota_subsp._carota_652393.bam (621.8 Mb)
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Title Daucus_carota_subsp._carota_Ames_27395
Downloaded 3 times
Description Bam 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 != "*"' >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 >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
Download Daucus_carota_subsp._carota_Ames_27395.bam (480.4 Mb)
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Title Daucus_carota_subsp._gummifer_478883
Downloaded 4 times
Description Bam 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 != "*"' >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 >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
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Title Daucus_carota_subsp._gummifer_Ames_26381
Downloaded 2 times
Description Bam 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 != "*"' >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 >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
Download Daucus_carota_subsp._gummifer_Ames_26381.bam (335.1 Mb)
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Title Daucus_carota_subsp._gummifer_Ames_26383
Downloaded 2 times
Description Bam 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 != "*"' >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 >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
Download Daucus_carota_subsp._gummifer_Ames_26383.bam (532.3 Mb)
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Title Daucus_carota_subsp._gummifer_Ames_31194
Downloaded 2 times
Description Bam 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 != "*"' >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 >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
Download Daucus_carota_subsp._gummifer_Ames_31194.bam (480.7 Mb)
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Title Daucus_carota_subsp._maximus_Ames_26408
Downloaded 2 times
Description Bam 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 != "*"' >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 >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
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Title Daucus_conchitae_652367
Downloaded 4 times
Description Bam 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 != "*"' >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 >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
Download Daucus_conchitae_652367.bam (803.6 Mb)
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Title Daucus_conchitae_652375
Downloaded 2 times
Description Bam 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 != "*"' >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 >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
Download Daucus_conchitae_652375.bam (187.5 Mb)
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Title Daucus_conchitae_652385
Downloaded 2 times
Description Bam 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 != "*"' >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 >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
Download Daucus_conchitae_652385.bam (186.4 Mb)
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Title Daucus_crinitus_652412
Downloaded 2 times
Description Bam 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 != "*"' >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 >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
Download Daucus_crinitus_652412.bam (352.4 Mb)
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Title Daucus_crinitus_652413
Downloaded 2 times
Description Bam 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 != "*"' >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 >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
Download Daucus_crinitus_652413.bam (288.7 Mb)
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Title Daucus_glochidiatus_285038
Downloaded 2 times
Description Bam 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 != "*"' >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 >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
Download Daucus_glochidiatus_285038.bam (320.3 Mb)
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Title Daucus_guttatus_286611
Downloaded 2 times
Description Bam 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 != "*"' >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 >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
Download Daucus_guttatus_286611.bam (244.3 Mb)
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Title Daucus_guttatus_652233
Downloaded 2 times
Description Bam 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 != "*"' >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 >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
Download Daucus_guttatus_652233.bam (323.0 Mb)
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Title Daucus_involucratus_652332
Downloaded 2 times
Description Bam 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 != "*"' >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 >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
Download Daucus_involucratus_652332.bam (277.0 Mb)
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Title Daucus_involucratus_652350
Downloaded 4 times
Description Bam 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 != "*"' >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 >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
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Title Daucus_littoralis_295857
Downloaded 2 times
Description Bam 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 != "*"' >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 >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
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Title Daucus_muricatus_295863
Downloaded 4 times
Description Bam 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 != "*"' >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 >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
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Title Daucus_muricatus_Ames_29090
Downloaded 2 times
Description Bam 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 != "*"' >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 >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
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Title Daucus_pusillus_349267
Downloaded 3 times
Description Bam 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 != "*"' >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 >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
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Title Daucus_pusillus_661242
Downloaded 2 times
Description Bam 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 != "*"' >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 >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
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Title Daucus_setulosus_652329
Downloaded 2 times
Description Bam 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 != "*"' >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 >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
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Title Daucus_setulosus_652360
Downloaded 3 times
Description Bam 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 != "*"' >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 >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
Download Daucus_setulosus_652360.bam (329.3 Mb)
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Title Daucus_syrticus_Ames_29096
Downloaded 2 times
Description Bam 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 != "*"' >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 >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
Download Daucus_syrticus_Ames_29096.bam (862.9 Mb)
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Title Daucus_syrticus_Ames_29108
Downloaded 3 times
Description Bam 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 != "*"' >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 >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
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Title Daucus_tenuisectus_Ames_31616
Downloaded 5 times
Description Bam 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 != "*"' >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 >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
Download Daucus_tenuisectus_Ames_31616.bam (1.781 Gb)
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Title Oenanthe_virgata_Ames_30293
Downloaded 3 times
Description Bam 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 != "*"' >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 >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
Download Oenanthe_virgata_Ames_30293.bam (233.4 Mb)
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Title Pseudorlaya_pumila_662301
Downloaded 2 times
Description Bam 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 != "*"' >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 >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
Download Pseudorlaya_pumila_662301.bam (771.9 Mb)
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Title Rouya_polygama_674284
Downloaded 1 time
Description Bam 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 != "*"' >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 >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
Download Rouya_polygama_674284.bam (795.0 Mb)
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When using this data, please cite the original publication:

Spooner DM, Ruess H, Iorizzo M, Senalik D, Simon P (2017) Entire plastid phylogeny of the carrot genus ( Daucus , Apiaceae): Concordance with nuclear data and mitochondrial and nuclear DNA insertions to the plastid. American Journal of Botany 104(2): 296-312. http://dx.doi.org/10.3732/ajb.1600415

Additionally, please cite the Dryad data package:

Spooner DM, Ruess H, Iorizzo M, Senalik D, Simon P (2017) Data from: Entire plastid phylogeny of the carrot genus (Daucus, Apiaceae): Concordance with nuclear data and mitochondrial and nuclear DNA insertions to the plastid. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.cv4r7
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