NextGENe Online Help : NextGENe Viewer : Mitochondrial Amplicon Analysis Project : Mitochondrial Amplicon project report
Mitochondrial Amplicon project report
After you open a Mitochondrial amplicon analysis project in the NextGENe viewer, an MT Show Mitochondrial Amplicon Report option is displayed on the Report Selection icon. Select this option to open the Mitochondrial Amplicon report in addition to the Alignment view. The report has two sections. The top section is the Amplicon report, which shows the different amplicons that were analyzed along with associated information for each amplicon. The bottom section is the Allele report, which displays a row for each allele by name that was identified in the sample for a selected amplicon. Double-click any entry in the Amplicon report to update the display in the NextGENe viewer and the Allele report accordingly. You can also double-click any allele in the Allele report to change the focus of the display to the selected allele.
  
Field
Description
Amplicon report
Amplicon
The name of the amplicon that was analyzed. Any amplicons that failed any of the Filter settings for the report are grouped into a row with Unknown displayed in this column. See Mitochondrial Amplicon project report.
Amplicon Coverage
The total number of reads that were aligned to the amplicon.
Amplicon Percentage
Amplicon coverage/Total number of aligned reads.
Allele Number
The total number of alleles that were identified for the amplicon.
Allele Frequency
The number of reads that were assigned to each allele out of the number of reads that were assigned to all accepted alleles for the amplicon. (Shown as a percentage.)
Note: Depending on the Filter settings that were specified for the report, these values might not be the same as the Frequency values in the Allele report. See Mitochondrial Amplicon project report.
Allele Total Coverage
The total number of reads that are assigned to each allele.
Allele report
Sequence
The sequence for the sample allele.
Start
The start position of the allele within the reference.
End
The end position of the allele within the reference.
Frequency
The number of reads that were assigned to the allele out of the total number of reads that were aligned to the amplicon. (Shown as a percentage.)
Note: Depending on the Filter settings that were specified for the report, these values might not be the same as the Allele Frequency values in the Amplicon report. See Mitochondrial Amplicon Report settings dialog box.
Total Reads
The total number of reads that aligned to the allele.
Forward Reads
The number of reads that were assigned to the allele that were forward reads.
Reverse Reads
The number of reads that were assigned to the allele that were reverse reads.
Differences
The number of bases in the sample allele sequence that do not match the reference allele sequence.
By default, when the Mitochondrial Amplicon report first opens in the NextGENe viewer, it is displayed on the right side of the opened viewer, and the focus in the Alignment viewer is set to the first amplicon in the list of analyzed amplicons. A blue cross centered in the Alignment viewer indicates the position of the amplicon. The Allele report details the alleles that were identified for this first amplicon. You can click the Switch Report Layout icon on the NextGENe Viewer toolbar to select the location for showing the report (to the right or at the bottom of the NextGENe Viewer), or to elect to show only the report (the Alignment viewer is hidden), or to hide the report.
The Mitochondrial Amplicon report is interactive. You can:
• Double-click on any amplicon to change the focus in the Alignment view to that of the selected amplicon. The Allele report display is updated accordingly.
• Double-click on any allele to change the focus in the Alignment viewer to that of the selected allele. A blue cross is displayed in the Alignment viewer to indicate the position of the selected allele on the locus.
Other options are available on the report toolbar. See Mitochondrial Amplicon analysis project report toolbar.