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. 2018 Jul 13;6:e5175. doi: 10.7717/peerj.5175

Figure 3. Reference-based assembly including heterozygous sites.

Figure 3

BAM-assembly file as generated with the SECAPR reference_assembly function, shown exemplarily for one exon locus (1/837) of one of the Geonoma samples (1/17). The displayed assembly contains all FASTQ sequencing reads that could be mapped to the reference sequence. The reference sequence in this case is the de-novo contig that was matched to the reference exon ‘Elaeis 1064 3’. DNA bases are color-coded (A, green; C, blue; G, black; T, red). The enlarged section contains a heterozygous site, which likely represents allelic variation, as both variants A and G are found at approximately equal ratio.