Save SNP consensus sequence
Click Save SNP consensus sequence to open the SNP Consensus Sequence Options dialog box. The dialog box contains options for specifying how you want to save the SNP consensus sequence.
 | Optionally, you can click Load Settings on the dialog box, and browse to and select a Settings file (.ini file) to generate the Save SNP Consensus Sequence report based on the saved settings in the file. |
Load SNP File | Select this option to load a tab-delimited text file that lists specific variant positions that are to be used for saving the SNP consensus sequence. The first line in the file is the Title line. The file has the following format, where the backslash (\) indicates a tab: Chr\tChr Position\tRef_Allele\tSample_Allele\n Example: 1\t100\tA\tG\n |
• SNP | • Output a consensus sequence to a file that shows both alleles present at SNP positions, where, for example: • A/A indicates a homozygous change to A. • A/C indicates a heterozygous change with both A and C found at the position. |
• Fasta | • Output a consensus sequence to a file that: • Shows only a single allele present for a homozygous position. For example, A indicates a homozygous change to A. • Uses IUPAC characters for heterozygous positions. For example, M indicates a heterozygous change with both A and C found at the position. |
Note: For either selection, covered regions are exported as defined by the Output Consensus Sequence settings below. | |
Before or After SNP | Determines the number of bases on either side of each variant that are to be included in the SNP consensus sequence when it is generated. |
Output Consensus Sequence | |
Homozygote(0%-100.0%) | The minimum percentage of reads that have an allele for the allele to be considered homozygous. For example, if this value is set to 80% and 85% of reads aligned at the location identified as a SNP show a “G” while 15% show a “T,” the position is considered homozygous and the consensus sequence shows a G/G at the location if SNP is selected and only a “G” at the location if the Fasta option is selected. |
IUPAC Heterozygote(0%-100.0%) | The requirements for a location to be considered heterozygous. More than one nucleotide must observed above the set percentage for the location to be considered heterozygous. For example, if this value is set to 25% and 65% of reads aligned at the location identified as a SNP show a “G” while 35% show a “T,” the location is considered heterozygous and the consensus sequence shows a G/T at the location if the SNP is selected and only a “K” (which is the IUPAC symbol for G and T) at the location if the Fasta option is selected. |
Homozygote Indel(20.00%-100%) | The percentage of reads that are aligned at the variant location that must contain the indel for the indel to be included in the consensus sequence. |