GS Reporter Metric File Contents Descriptions

6.5	GS Reporter Metric File Contents Descriptions

gsReporter Output Metrics File Contents:

454RuntimeMetricsAll / 454AllControlMetrics	454QualityFilterMetrics	454BaseCallerMetrics
Comment Header software version Run Name Analysis Name Region Name Key sequences file creation timestamp	Comment Header software version Run Name Analysis Name file creation timestamp	Comment Header software version file creation timestamp
Run Conditions Group Date Run Name Analysis Name PTP Type Analysis Type Number of regions Number of cycles Flow Order	Run Conditions Group Date Run Name Analysis Name	Run Parameters Group Analysis Name
Region Group Region Name Number of raw wells Number of Key Pass wells Key Group	Region Group Region Name Number of raw wells Number of Key Pass wells Key Group	BaseCaller Results Number of reads Average read length Standard deviation of read length
Key Group* Key sequence numKeyPass Key signal per base ppi1, ppi2, ppi3 (avg signal, std dev.) *For the 454AllControlMetrics file, this group contains the combined metrics from all control reads.	Key Group Key sequence numKeyPass numDotFailed numMixedFailed numTrimmedTooShortQuality numTrimmedTooShortPrimer totalPassFiltering	Region Key Group Region Name Key sequence Number of reads totalPassFiltering Average read length Average quality score Length histogram group (length bin counts) Quality Histogram Group (quality bin count)

Timestamps:

Convention	Description
YYYY/MM/DD HH:MM:SS or YYYY_MM_DD_hh_mm	YYYY - four digit year MM - two digit month (01 to 12) DD - two digit day (01 to 31 depending on month) hh - two digit hour (00 to 23) mm - two digit minutes (00 to 59)

Names and Strings:

Convention	Description
Rig Name	Network host name of the computer in the GS FLX+ Instrument or the GS Junior Attendant PC.
User Name	Name of the user who executed the Run (from the GS Sequencer sign in)
freeForm	Any alpha numeric string (“Unique Run name”) that was entered by the user for the sequencing Run
AnalType	String identifying the data processing type that was run. “imageProcessingOnly”, for example, contains the image processed results.

Directory Names:

Type	Convention	Description
Run Name	R_YYYY_MM_DD_hh_mm_rigName_userName_freeForm	R_ stands for “Run”, the rest defined above
Analysis Name	D_YYYY_MM_DD_hh_mm_rigName_userName_AnalType or D_YYYY_MM_DD_hh_mm_rigName_userName_freeForm	D_ stands for “Data”, a the rest defined above

Comment Header Definitions:

Information	Description
Software Version	Version of the Data Analysis Software invoked
Run Name	R_YYYY_MM_DD_hh_mm_rigName_userName_freeForm
Analysis Name	D_YYYY_MM_DD_hh_mm_rigName_userName_AnalType or D_YYYY_MM_DD_hh_mm_rigName_userName_freeForm
Region Name	A number valid for the number of loading regions on the PicoTiterPlate Device, e.g. for a two region device the region name can be ‘1’ or ‘2’.
Key Sequences	Four base adaptor sequences for Library and Control beads
Timestamp	YYYY/MM/DD HH:MM:SS

Run Group Definitions:

Information	Description
Date	File creation timestamp in the form: YYYY/MM/DD hh:mm
Run Name	R_YYYY_MM_DD_hh_mm_rigName_userName_freeForm
Analysis Name	D_YYYY_MM_DD_hh_mm_rigName_userName_AnalType or D_YYYY_MM_DD_hh_mm_rigName_userName_freeForm
PTP Type	Currently set to “unknown”.
Analysis type	Currently set to “<analysisType goes here>”.
Number of regions	The number of physically separate regions present on the PicoTiterPlate Device (as defined by the Bead Deposition Gasket used during PTP Device preparation). This value was set by the user during the sequencing Run setup. Data from each region is processed separately, and each region has a complete set of metrics.
Number of cycles	Currently set to -1.
Flow order	Currently set to “<flowOrder goes here>”.
User Name	Name of the user who executed the Run (from the GS Sequencer sign in)
Region Group	A sub group containing region information, described below.

Region Group Definitions:

Information	Description
Region name	A number valid for the number of loading regions on the PicoTiterPlate Device, e.g. for a two region device the region name can be ‘1’ or ‘2’.
Number of Raw wells	The number of raw wells detected in this region of the PicoTiterPlate Device. These are wells that are generating enough signal to be considered for further processing.
Number of Key Pass Wells	The total number of wells where the first four bases called match any defined key, detected in this region of the PicoTiterPlate Device. A key pass well is assumed to contain a legitimate DNA read. The key pass wells are the wells that are further processed in the downstream data analysis pipeline.
Key Group	A sub group containing key information, described below.

The key subgroup is contained in the region group. The key sequence for sample library reads is GACT, TCAG and for Control DNA reads is CATG or ATGC (see Section 7.1 for details on Control DNA keys). This corresponds to the first four nucleotides in a read. This is dictated by the keys present (1) on Adaptors used to generate the DNA library and (2) on the Control DNA Beads provided in the GS Sequencing Kits. The keywords contained in the key group are:

Key Group Definitions:

Information	Description
Key sequence	First three bases of the actual key sequence; ‘GAC’ or ‘TCA’ for library reads and for Control DNA reads ‘CAT’ or ‘ATG’ (see Section 7.1 for details)
numKeyPass	The number of wells identified on the PicoTiterPlate Device with a valid key sequence. A Key Pass well is assumed to contain a legitimate DNA read and is further processed in the downstream data analysis pipeline.
Key signal per base	A comma-separated list providing the average signal per base for the key signals and the corresponding standard deviation.
ppi1, ppi2, ppi3…	A set of comma-separated lists providing the average signal and the corresponding standard deviation, for each normalization flow during the sequencing Run.
numDotFailed	The number of reads that failed the ‘dot’ filter; reads with too many negative flows. (Section 1.4.2)
numMixedFailed	The number of reads that failed the ‘mixed’ filter; reads with too many positive flows. (Section 1.4.2)
numTrimmedTooShortQuality	The number of reads that failed the length test because of quality trimming. (Section 0)
numTrimmedTooShortPrimer	The number of reads that failed the length test because of Primer sequence trimming. (Section 0)
totalPassFiltering	The number of wells that passed all five filters in the Signal Processing application. These are the wells that contain high quality DNA reads that are used (as trimmed) as input for data analysis post-Run processing, or for basecalling of the reads.

BaseCaller Results Group Definitions:

Information	Description
Number of Reads	Number of reads from the wells that passed all five filters in the Signal Processing application.
Average Read Length	Average length across all reads that passed all five filters in the Signal Processing application.
Std Dev of Avg. Read Length	Standard deviation of the average length across all reads that passed all five filters in the Signal Processing application.

Region Key Group Definitions:

Information	Description
Region name	A number corresponding a loading region on the PicoTiterPlate Device, e.g. for a two region PTP Device the region name can be ‘1’ or ‘2’.
Key sequence	First three bases of the actual key sequence; ‘TCA’ for library reads and for Control DNA reads ‘CAT’ or ‘ATG’ (see Section 7.1 for details)
Number of Reads	The total number of DNA reads that were retained (passed) after all quality filters were applied in this region with the specified key.
totalBases	Total number of DNA bases in the filtered reads (after trimming).
Average Read Length	A comma-separated list providing the average length of the DNA reads after filtering and trimming, and the corresponding standard deviation.
Average Quality Score	A comma-separated list providing the average quality score of all the DNA bases in these filtered reads (after trimming), and the corresponding standard deviation.
Length Histogram Group	A subgroup located within the regionKey group which provides a comma-separated list of the number of filtered reads at each read length observed in this region and with this sequencing key. Thus, on each line; a keyword, the read length (for the abscissa of the histogram), and the number of filtered reads with this trimmed read length.
Quality Histogram Group	A subgroup located within the regionKey group which provides a comma-separated list of the number of bases called at each quality score observed in this region and with this sequencing key. Thus, on each line; a keyword, the quality score (for the abscissa of the histogram), followed by the number of bases with this quality score.