Jaya Prakash Finishing Paper

Jaya Prakash Dr. Elgin, Dr. Shaffer Biology 434W 10 February 2017 Finishing of DEUG4927010 Abstract The goal of this project was to prepare the DEUG4927010 contig—which covers the terminal 99,279 bases from the fourth chromosome of Drosophila eugracilis—for annotation. In the initial assembly of this project, there were 122 high quality discrepancies and 49 regions with low depth of coverage. Ninety one MNRs were present in low depth of coverage regions, and 67 MNRs were found near highly discrepant positions. There were no low consensus quality regions. Overall, 29 edits were made to the consensus sequence by using ‘base counting’ and ‘Illumina prioritization’ strategies, which are defined and explained in the High Quality Discrepancies (HQDs) section. Two potential SNPs were identified and tagged at positions 98,587 as well as 98,764. Finally, a third highly discrepant position at 99,103 was found within a repeat element of the contig. Primers for this site were designed to determine whether variation in the base was the result of deviation in the repeat, a SNP, or a misassembly. This project is now ready for annotation.