Metrics
Category Metrics
Overview
Metrics produced by the ExtractIlluminaBarcodes program that is used to parse data in the basecalls directory and determine to which barcode each read should be assigned.This table summarizes the values that are specific to this metric.
| Metric | Summary |
|---|---|
| BARCODE | The barcode (from the set of expected barcodes) for which the following metrics apply. Note that the "symbolic" barcode of NNNNNN is used to report metrics for all reads that do not match a barcode. |
| BARCODE_WITHOUT_DELIMITER | |
| BARCODE_NAME | The barcode name. |
| LIBRARY_NAME | The name of the library |
| READS | The total number of reads matching the barcode. |
| PF_READS | The number of PF reads matching this barcode (always less than or equal to READS). |
| PERFECT_MATCHES | The number of all reads matching this barcode that matched with 0 errors or no-calls. |
| PF_PERFECT_MATCHES | The number of PF reads matching this barcode that matched with 0 errors or no-calls. |
| ONE_MISMATCH_MATCHES | The number of all reads matching this barcode that matched with 1 error or no-call. |
| PF_ONE_MISMATCH_MATCHES | The number of PF reads matching this barcode that matched with 1 error or no-call. |
| PCT_MATCHES | The fraction of all reads in the lane that matched to this barcode. |
| RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT | The rate of all reads matching this barcode to all reads matching the most prevalent barcode. For the most prevalent barcode this will be 1, for all others it will be less than 1 (except for the possible exception of when there are more orphan reads than for any other barcode, in which case the value may be arbitrarily large). One over the lowest number in this column gives you the fold-difference in representation between barcodes. |
| PF_PCT_MATCHES | The fraction of PF reads in the lane that matched to this barcode. |
| PF_RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT | The rate of PF reads matching this barcode to PF reads matching the most prevalent barcode. For the most prevalent barcode this will be 1, for all others it will be less than 1 (except for the possible exception of when there are more orphan reads than for any other barcode, in which case the value may be arbitrarily large). One over the lowest number in this column gives you the fold-difference in representation of PF reads between barcodes. |
| PF_NORMALIZED_MATCHES | The "normalized" matches to each barcode. This is calculated as the number of pf reads matching this barcode over the sum of all pf reads matching any barcode (excluding orphans). If all barcodes are represented equally this will be 1. |
GATK version 4.6.0.0 built at Sat, 29 Jun 2024 20:47:29 -0400.
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