Save consensus sequence
Click Save Consensus Sequence to open the Save Consensus Sequence Options dialog box. By default, the General tab is the open tab. The tab displays the options for specifying how you want to save the 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 Consensus Sequence report based on the saved settings in the file. |
• Setting
Option | Description |
|---|---|
All | Export all bases in the consensus sequence as one segment in a fasta file. If no reads align to a region in the reference genome, then the reference sequence is exported for the region. Covered regions are exported as defined by the Output Consensus Sequencesettings below. |
Covered | Export a consensus sequence that contains the consensus bases from only the covered regions of the reference sequence. Multiple segments are generated and placed into a single fasta file. Each segment represents a continuous region of adequate coverage. Covered regions are exported as defined by the Output Consensus Sequence settings below. If no reads are aligned to a region in the reference sequence, then no consensus sequence is output for the region. |
Uncovered | Export a consensus sequence that contains bases from only the uncovered regions of the reference sequence. Multiple segments are generated and placed into a single fasta file. Each segment represents a continuous region that has no coverage. Regions of the reference sequence to which sequence reads are aligned are not included in the output. |
• Coverage options
Options | Description |
|---|---|
Specify the coverage region for which you want to save the coverage settings. You can do one of the following: | |
• Input Region Manually | Input the region manually. (You must specify the starting position and the ending position.) |
• Input Points of Interest Text File (*.txt) | There are no special requirements for uploading a comma-delimited text file. If the input text file is a comma-delimited text file, it must contain one of the following lists: • Specific reference locations (position number or a range of positions (start position number - end position number)) separated by commas • A list of reference gene names separated by commas |
• Input Region of Interest BED File (*.BED) | • A BED file is a tab-delimited text file. You can upload a BED file only if the reference sequence contains chromosome information, which means that the reference sequence must be either a preloaded reference that NextGENe supplies, or a GenBank reference file that contains chromosome information |
• Output Consensus Sequence
Option | Description |
|---|---|
Homozygote(0%-100.0%) | The minium 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 only a “G” at the location. |
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 “K” (which is the IUPAC symbol for G and T) at the location. |
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. |