Ion AmpliSeq™ HD Custom panel files
The following files are available for download for custom Ion AmpliSeq™ HD DNA gene designs. The results files are available for submitted designs only, in the Results ready screen.
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A PNG image of a histogram that represents the distribution of amplicon insert sizes, excluding undigested forward and reverse primer sequences and barcode adapters. |
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A PNG image of a histogram that represents the distribution of amplicon sizes, including undigested forward and reverse primer sequences and barcode adapters. |
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A CSV file that contains exon-level coverage details, including target bases, number of amplicons that are required to cover the exon, number of bases covered by the amplicons, and percent coverage per each coordinate region. Note: Any regions submitted using the Region input type (chromosome start/end coordinates) is NOT be displayed in this results file (see callout 1 in Figure 1). |
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A CSV file that contains statistics for covered bases, overall coverage, and number of exons per gene or genomic region. Per gene or genomic region, the coverage summary file includes the total number of amplicons, total bases submitted, bases that were covered, and the overall coverage (Covered bases÷Total Bases). The file also contains the number of exons in each entry point as well as a distribution of the number of exons that were covered at 1, >0.95, >0.9, >0.8, >0.7, >0.5, >0.2, >0.2 and at 0. These are displayed as a percentage in the UI. |
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A BED file that defines genomic coordinates that are targeted by the primers. The data in this file appears as the CoveredBases_AmpliSeqID_<panel ID> track that is shown in green when you link directly to the UCSC Genome Browser to review results. |
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A BED file that contains genomic coordinates the primers are designed to target. For each amplicon ID in the panel, the file lists the chromosome number, the insert start, the insert end, and the gene symbol (if provided in the submitted file). The data in this file appears as the InputTargets_AmpliSeqID_<panel ID> track that is shown in blue when you link directly to the UCSC Genome Browser to review results. |
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A BED file that contains hotspot genomic coordinates that are covered by the <panel ID>_ Designed.bed file. |
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A BED file that contains the regions that were missed in the design. The data in this file appears as the MissedBases_AmpliSeqID_<panel ID> track that is shown in red when you link directly to the UCSC Genome Browser to review results. |
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A CSV file that contains the data for the 384‑well plate. The first column contains pool information and the plate ID of the panel. The second and third columns contain the coordinates within the 384‑well plate, where each amplicon is located. Additionally, the file contains the Amplicon ID, the gene symbol, amplicon genomic coordinates (or the coordinates of the genomic region), and start and stop genomic coordinates of the insert for each amplicon in the panel. |
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A JSON file that contains information to automatically configure a run plan for a panel in Torrent Suite™ Software. |