Editing Final Report/Thesis 2019 (section)

===DNA reference file===
A DNA reference file stores a group of SNPs data of owner's DNA. The format of DNA reference files used in this project are of the same format which is 23andMe company's file, where 23andMe is a company that attended to provide personal genetic information for customers by using advanced genetic analysis techniques and web-based interactive tools. A screenshot of a sample file is shown below.
[[File:Dna_ref.png|thumb|center|300px|Figure 5: Sample DNA file from 23andMe]]
As shown in the figure, there are 4 columns in the DNA reference file: rsid, chromosome, position and genotype. The rsid is a unique id used to identify a specific SNP.
The format of rsid starts with “rs” and followed by a number (eg. rs123456). These rsids are commonly used by researchers and databases. There is another special format of rsid that starts with “i” and followed by a number (eg. i123456). This “i” format is used internally by 23andMe to identify the unknown SNP and cannot be used in public database. The second column chromosome identify which chromosome the SNP belongs to (1st to 22nd chromosome). The third column, position, indicates positions of SNPs in owner's DNA sequence. The last column, genotype, is the column for base pairs of variants (A, T, G, C). Note that there are some cases where the genotype result for some SNPs are not able be provided and “--” would be displayed in genotype column. It is important to note that only the SNPs with identified base pairs can be used for DNA analysis.