CSV Metrics File Format

A Comma-Separated Value (CSV) file is a universal text file format for storing data. You can download an analysis metrics CSV file that contains analysis-level information for one or more Torrent Suite™ Software analysis runs, in the Torrent Browser Projects > ProjectsName > Results Sets in ProjectName page.

In the CSV file, each line represents a Torrent Suite™ Software analysis run, and within each line information fields are separated by a comma. These files are easily opened using spreadsheet software, such as Microsoft™ Office Excel™ or OpenOffice.org Calc, where each comma-separated field is listed in a separate column. The Torrent Browser CSV file has many CSV fields per entry, as described in the following table:

Field	Description
Report	Name of the analysis run report
Status	Status of the analysis (e.g., 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
Library_100Q10_Reads	Reads of length at least 100bp with 90% or greater accuracy
Library_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 50bp with 99% or greater accuracy
Library_100Q20_Reads	Reads of length at least 100bp with 99% or greater accuracy
Library_200Q20_Reads	Reads of length at least 200bp 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_Alignment	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 50bp
Library_100Q47_Reads	Number of perfect reads of length at least 100bp
Library_200Q47_Reads	Number of perfect reads of length at least 200bp
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
PGM Name	Name of the Ion PGM™ or Ion Proton™ instrument where the sample was sequenced
Run Date	Date the sample was sequenced
Run Directory	Location of the raw DAT files on the Torrent Server
Num_Washouts	NA
Num_Dud_Washouts	NA
Num_Washout_Ambigous	NA
Num_Washout_Live	NA
Num_Washout_Test_Fragment	NA
Num_Washout_Library	NA
Library_Pass_Basecalling	NA
Library_pass_Cafie	NA
Number_Ambiguous	NA
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	JSON string of plugin data
s	JSON string of plugin data

* Columns 4-11 contain test fragment metric. There is one row of metrics for each test fragment: A through D. The other columns contain library read metrics.