Analysis metrics file fields

In the analysis metrics file, each line represents a Torrent Suite™ Software analysis run. Within each line, fields are separated by a comma. Each comma-separated field is listed in a separate column. You can open the files with spreadsheet software such as Microsoft™ Excel™ or Apache^® OpenOffice ™ Calc.

The file has many fields per entry. Rows 4 through 11 (marked by *) contain test fragments metrics. The other rows contain library read metrics.

Field	Description
`Report`	Name of the analysis run report.
`Status`	Status of the analysis (for example, Started, Complete).
`Flows`	Number of flow cycles from the actual sequencing run.
`TF Name`*	Test Fragment Name.
`Q10 Mean`*	Average Q10 read length.
`Q17 Mean`*	Average Q17 read length.
`System SNR`*	System Signal-to-Noise Ratio.
`50Q10 Reads`*	Number of TF Ion Sphere™ Particles (ISP) at 50+ bp at Q10.
`50Q17 Reads`*	Number of TF Ion Sphere™ Particles (ISP) at 50+ bp at Q17.
`Keypass Reads`*	Number of reads that have test fragment keys.
`TF Key Peak Counts`*	Signal strength of the first three bases of the TF key.
`Total_Num_Reads`	Total number of reads.
`Library_50Q10_Reads`	Reads of length at least 50bp with 90% or greater accuracy.
L`ibrary_100Q10_Reads`	Reads of length at least 100bp with 90% or greater accuracy.
L`ibrary_200Q10_Reads`	Reads of length at least 200bp with 90% or greater accuracy.
`Library_Mean_Q10_Length`	Average length of reads with 90% or greater accuracy.
`Library_Q10_Coverage`	Average per base coverage considering reads with 90% or greater accuracy.
`Library_Q10_Longest_Alignment`	Longest read length amongst reads with 90% or greater accuracy.
`Library_Q10_Mapped Bases`	Total bases from reads with 90% or greater accuracy.
`Library_Q10_Alignments`	Number of alignments from reads with 90% or greater accuracy.
`Library_50Q17_Reads`	Reads of length at least 50bp with 98% or greater accuracy.
`Library_100Q17_Reads`	Reads of length at least 100bp with 98% or greater accuracy.
`Library_200Q17_Reads`	Reads of length at least 200bp with 98% or greater accuracy.
`Library_Mean_Q17_Length`	Average length of reads with 98% or greater accuracy.
`Library_Q17_Coverage`	Average per base coverage considering reads with 98% or greater accuracy.
`Library_Q17_Longest_Alignment`	Longest read length amongst reads with 98% or greater accuracy.
`Library_Q17_Mapped Bases`	Total bases from reads with 98% or greater accuracy.
`Library_Q17_Alignments`	Number of alignments from reads with 98% or greater accuracy.
`Library_50Q20_Reads`	Reads of length at least 50 bp with 99% or greater accuracy.
`Library_100Q20_Reads`	Reads of length at least 100 bp with 99% or greater accuracy.
`Library_200Q20_Reads`	Reads of length at least 200 bp with 99% or greater accuracy.
`Library_Mean_Q20_Length`	Average length of reads with 99% or greater accuracy.
`Library_Q20_Coverage`	Average per base coverage considering reads with 99% or greater accuracy.
`Library_Q20_Longest_Alignmen`t	Longest read length amongst reads with 99% or greater accuracy.
`Library_Q20_Mapped_Bases`	Total bases from reads with 99% or greater accuracy.
`Library_Q20_Alignments`	Number of alignments from reads with 99% or greater accuracy.
`Library_Key_Peak_Counts`	Signal strength of the first three bases of the library key.
`Library_50Q47_Reads`	Number of perfect reads of length at least 50 bp.
`Library_100Q47_Reads`	Number of perfect reads of length at least 100 bp.
`Library_200Q47_Reads`	Number of perfect reads of length at least 200 bp.
`Library_Mean_Q47_Length`	Average length of perfect reads.
`Library_Q47_Coverage`	Average per-base coverage considering only perfect reads.
`Library_Q47_Longest_Alignment`	Longest reads length amongst perfect reads.
`Library_Q47_Mapped_Bases`	Total bases from perfect reads.
`Library_Q47_Alignments`	Number of alignments from perfect reads.
`Library_CF`	CAFIE metric: Carry forward.
`Library_IE`	CAFIE metric: Incomplete extension.
`Library_DR`	CAFIE metric: Signal/polymerase loss (droop).
`Library_SNR`	System signal-to-noise ratio.
`Sample`	Name of the sample.
`Library`	Name of the reference genome.
`Notes`	Any additional user-provided notes.
`Run Name`	Long name of the analysis run.
`Run Date`	Date that the sample was sequenced.
`Run Directory`	Location of the raw DAT files on the Ion Torrent™ Server.
`Num_Washouts`	Deprecated field. Value for this field is 0 in CSV file.
`Num_Dud_Washouts`	Deprecated field. Value for this field is 0 in CSV file.
`Num_Washout_Ambigous`	Deprecated field. Value for this field is 0 in CSV file.
`Num_Washout_Live`	Deprecated field. Value for this field is 0 in CSV file.
`Num_Washout_Test_Fragment`	Deprecated field. Value for this field is 0 in CSV file.
`Num_Washout_Library`	Deprecated field. Value for this field is 0 in CSV file.
`Library_Pass_Basecalling`	Deprecated field. Value for this field is 0 in CSV file.
`Library_pass_Cafie`	Deprecated field. Value for this field is 0 in CSV file.
`Number_Ambiguous`	Deprecated field. Value for this field is 0 in CSV file.
`Number_Live`	Number of wells producing a signal.
`Number_Dud`	Number of wells with ISPs but no signal.
`Number_TF`	Number of wells containing test fragment.
`Number_Lib`	Number of wells containing library.
`Number_Bead`	Number of wells containing beads.
`Library_Live`	Number of wells containing library ISP with signal.
`Library_Keypass`	Number of wells containing library ISP with signal and match key.
`TF_Live`	Number of wells containing test fragment ISP with signal.
`TF_Keypass`	Number of wells containing test fragment ISP with signal and match key.
`Keypass_All_Beads`	Number of wells containing ISP with signal and match key.
`P`	Plugin data output in JSON format. The structured text format includes named fields.
`s`	Status of plugin data output in JSON format.

Contents

Index

Glossary

Search Results

Analysis metrics file fields