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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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[ICO]NameLast modifiedSizeDescription
[PARENTDIR]Parent Directory  -  
[   ]AlignedPrimers.bed.gz2017-07-25 15:13 1.0KAnnotation or junction file
[   ]AlignedPrimers.bed.gz.tbi2017-07-25 15:13 191 Tabix index file
[   ]Amplicons.bed.gz2017-07-25 15:13 223 Annotation or junction file
[   ]Amplicons.bed.gz.tbi2017-07-25 15:13 167 Tabix index file
[   ]SRR1528539.bam2017-07-25 15:13 23M 
[   ]SRR1528539.bam.bai2017-07-25 15:13 688  
[   ]SRR1528540.bam2017-07-25 15:13 35M 
[   ]SRR1528540.bam.bai2017-07-25 15:13 640  
[   ]SRR1528541.bam2017-07-25 15:13 6.3M 
[   ]SRR1528541.bam.bai2017-07-25 15:13 560  
[   ]SRR1531280.bam2017-07-25 15:13 23M 
[   ]SRR1531280.bam.bai2017-07-25 15:13 656  
[   ]SRR1531281.bam2017-07-25 15:13 32M 
[   ]SRR1531281.bam.bai2017-07-25 15:13 784  
[   ]SRR1531282.bam2017-07-25 15:13 13M 
[   ]SRR1531282.bam.bai2017-07-25 15:13 592  
[   ]SRR1531283.bam2017-07-25 15:13 41M 
[   ]SRR1531283.bam.bai2017-07-25 15:13 1.0K 
[   ]SRR1531284.bam2017-07-25 15:13 25M 
[   ]SRR1531284.bam.bai2017-07-25 15:13 672  
[   ]SRR1531285.bam2017-07-25 15:13 698K 
[   ]SRR1531285.bam.bai2017-07-25 15:13 360  
[   ]SRR1531286.bam2017-07-25 15:13 9.9K 
[   ]SRR1531286.bam.bai2017-07-25 15:13 192  
[   ]SRR1531287.bam2017-07-25 15:13 24M 
[   ]SRR1531287.bam.bai2017-07-25 15:13 736  
[   ]SRR1531288.bam2017-07-25 15:13 17M 
[   ]SRR1531288.bam.bai2017-07-25 15:13 704  
[   ]SRR1531289.bam2017-07-25 15:13 14M 
[   ]SRR1531289.bam.bai2017-07-25 15:13 640  
[   ]SRR1763770.bam2017-07-25 15:13 15M 
[   ]SRR1763770.bam.bai2017-07-25 15:13 736  
[   ]SRR1763771.bam2017-07-25 15:13 20M 
[   ]SRR1763771.bam.bai2017-07-25 15:13 768  
[   ]SRR1763772.bam2017-07-25 15:13 9.0M 
[   ]SRR1763772.bam.bai2017-07-25 15:13 624  
[   ]SRR1763773.bam2017-07-25 15:13 22M 
[   ]SRR1763773.bam.bai2017-07-25 15:13 560  
[   ]SRR1763774.bam2017-07-25 15:13 7.7M 
[   ]SRR1763774.bam.bai2017-07-25 15:13 592  
[   ]SRR1763775.bam2017-07-25 15:13 18M 
[   ]SRR1763775.bam.bai2017-07-25 15:13 672  
[   ]SRR1763776.bam2017-07-25 15:13 7.9M 
[   ]SRR1763776.bam.bai2017-07-25 15:13 560  
[   ]SRR1763777.bam2017-07-25 15:13 16M 
[   ]SRR1763777.bam.bai2017-07-25 15:13 592  
[   ]SRR1763778.bam2017-07-25 15:13 8.2M 
[   ]SRR1763778.bam.bai2017-07-25 15:13 592  
[   ]SRR1763779.bam2017-07-25 15:13 5.5M 
[   ]SRR1763779.bam.bai2017-07-25 15:13 560  
[   ]SRR1763780.bam2017-07-25 15:13 20M 
[   ]SRR1763780.bam.bai2017-07-25 15:13 672  
[   ]SRR1763781.bam2017-07-25 15:13 8.8M 
[   ]SRR1763781.bam.bai2017-07-25 15:13 608  
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