Then the tag value is a the Phred-scaled posterior probability that the On the other hand, if the value of the header-tag is Probability instead, For each barcode, the sum of the Smith-Waterman score is normalizedīy the length of the barcode times the match score, then multiplied by 100Īnd rounded this provides an integer value between 0 - 100. Smith-Waterman scores that support the call in the bc tag across all Then the tag represents the mean normalized sum of the calculated If the BarcodeQuality element of the header is set to Score, The integer ( int) bq tag contains the barcode call confidence.IntegerĬodes represent 0-based position in the FASTA file of barcodes. Succinctly, it contains the integer pair \(B_F, B_R\). Representing the inferred forward and reverse barcodes sequences (asĭetermined by their ordering in the Barcode FASTA), or more The bc tag contains the barcode call, a uint16.In the absence of barcodes, both the bc and If the tags are present for any subread in a ZMW, they must be presentįor all of them. Has the bc tag, it must also have a bq tag and vise-versa. The tags are also inter-depedent, so if a subread Subread belonging to a given ZMW should share identical bc andīq values. Both the bc and bq tags are calculated per-ZMW, so every.Non-subread records (scraps, ZMW read, CCS read, etc.) This tag is mandatory for subread records, but will be absent from ADAPTER_*_BAD flags can not be set unless the Likewise, some nearby barcode or insert bases may be missing or The adapter on this flank could be missingįrom the pbell molecule, or obscured by a local decrease in accuracy. That one or both adapters flanking this subread do not align to theĪdapter reference sequence(s). The ADAPTER_BEFORE_BAD and ADAPTER_AFTER_BAD flags indicate Subread is flanked by adapters or barcodes at the ends. The ADAPTER_* and BARCODE_* flags reflect whether the Subread in the ZMW, it will be available for all subreads in the
ToolsĬonsuming the BAM should be aware that orientation information mayīe unavailable for subreads in a ZMW, but if is available for any Subreads from a ZMW, neither orientation flag should be set. Is up to tools producing the BAM to determine whether to useĪdapters or barcodes to reckon the orientation, but if passĭirections cannot be confidently and consistently assessed for the Per-ZMW convention, defining one element of the asymmetricīarcode/adapter pair as the “front” and the other as the “back”. Is considered a “forward” or “reverse” pass is determined by a Otherwise these flags must be left unset. Only if either the adapters or barcode design is asymmetric, Orientation of a subread (designated by one of the mutuallyĮxclusive FORWARD_PASS or REVERSE_PASS bits) can be reckoned
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