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<title>Plastid genome resequencing project</title>
<h1>Plastid genome resequencing project</h1>
<p>
This directory contains data from BINF 6350 Genomic Biotechnology Lab,
developed and taught by Drs. Jennifer Weller and Cathy Moore, from
the Department of Bioinformatics and Genomics at UNC Charlotte.
</p>
<p>
Students performed a semester-long sequencing project in which they
used long-range PCR and an Ion Torrent sequencer to re-sequence
chloroplast genomes of tomato cultivars. Sequences are available
at the SRA as BioProject accessions <a
href="http://www.ncbi.nlm.nih.gov/bioproject/PRJNA256298">PRJNA256298</a>
and <a href="http://www.ncbi.nlm.nih.gov/bioproject/PRJNA256329">PRJNA256329</a>.
</p>
<p>
For amplicons and primers used in long-range PCR, see BED files Amplicons.bed.gz and Primers.bed.gz located in this directory.
</p>
<p>
BAM files in this directory were made by mapping sequence reads onto
onto the chloroplast genome (<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_007898.3">NC_007898.3</a>) using bowtie2 version 2.1.0 with the --local setting. For details, contact
Ivory Blakley in the Loraine Lab.
</p>
<p>
<p>Sequenced cultivars included:</p>
<p>
Baxter's Early Bush_a <a href="http://www.ncbi.nlm.nih.gov/sra/SRR1531281">(SRR1531281)</a>
<br>
Baxter's Early Bush_b <a href="http://www.ncbi.nlm.nih.gov/sra/SRR1763774">(SRR1763774)</a>
<br>
Black Cherry_a <a href="http://www.ncbi.nlm.nih.gov/sra/SRR1531284">(SRR1531284)</a>
<br>Black cherry_b <a href="http://www.ncbi.nlm.nih.gov/sra/SRR1763775">(SRR1763775)</a>
<br>Cherokee Purple_a <a href="http://www.ncbi.nlm.nih.gov/sra/SRR1531285">(SRR1531285)</a>
<br>Cherokee Purple_b <a href="http://www.ncbi.nlm.nih.gov/sra/SRR1763776">(SRR1763776)</a>
<br>Cherry_a <a href="http://www.ncbi.nlm.nih.gov/sra/SRR1528539">(SRR1528539)</a>
<br>Cherry_b <a href="http://www.ncbi.nlm.nih.gov/sra/SRR1763770">(SRR1763770)</a>
<br>Delicious_a <a href="http://www.ncbi.nlm.nih.gov/sra/SRR1531286">(SRR1531286)</a>
<br>Delicious_b <a href="http://www.ncbi.nlm.nih.gov/sra/SRR1763777">(SRR1763777)</a>
<br>German Cherry_a <a href="http://www.ncbi.nlm.nih.gov/sra/SRR1531282">(SRR1531282)</a>
<br>German Cherry_b <a href="http://www.ncbi.nlm.nih.gov/sra/SRR1763780">(SRR1763780)</a>
<br>Hardin's Miniature_a <a href="http://www.ncbi.nlm.nih.gov/sra/SRR1763773">(SRR1763773)</a>
<br>Hardin's Miniature_b <a href="http://www.ncbi.nlm.nih.gov/sra/SRR1531280">(SRR1531280)</a>
<br>Heinz 1706-BG_a <a href="http://www.ncbi.nlm.nih.gov/sra/SRR1531283">(SRR1531283)</a>
<br>Jersey Devil_a <a href="http://www.ncbi.nlm.nih.gov/sra/SRR1531287">(SRR1531287)</a>
<br>Jersey Devil_b <a href="http://www.ncbi.nlm.nih.gov/sra/SRR1763778">(SRR1763778)</a>
<br>LA2377_a <a href="http://www.ncbi.nlm.nih.gov/sra/SRR1763772">(SRR1763772)</a>
<br>Mortgage Lifter_a <a href="http://www.ncbi.nlm.nih.gov/sra/SRR1531289">(SRR1531289)</a>
<br>Mortgage Lifter_b <a href="http://www.ncbi.nlm.nih.gov/sra/SRR1763781">(SRR1763781)</a>
<br>Purple Calabash_a <a href="http://www.ncbi.nlm.nih.gov/sra/SRR1528540">(SRR1528540)</a>
<br>Purple Calabash_b <a href="http://www.ncbi.nlm.nih.gov/sra/SRR1763771">(SRR1763771)</a>
<br>Yellow Stuffer_a <a href="http://www.ncbi.nlm.nih.gov/sra/SRR1531288">(SRR1531288)</a>
<br>Yellow Stuffer_b <a href="http://www.ncbi.nlm.nih.gov/sra/SRR1763779">(SRR1763779)</a>
<br>Yellow Tomato_a <a href="http://www.ncbi.nlm.nih.gov/sra/SRR1528541">(SRR1528541)</a>
</p>
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