SAM specification

Header

@HD  VN:1.6  SO:unknown
@PG  ID:basecaller PN:dorado VN:0.2.4+3fc2b0f CL:dorado basecaller hac pod5/ DS:gpu:Quadro GV100

Read Group Header

Tag	Description
ID	<runid>_<basecalling_model>_<barcode_arrangement>
PU	<flow_cell_id>
PM	<device_id>
DT	<exp_start_time>
PL	ONT
DS	basecall_model=<basecall_model_name> modbase_models=<modbase_model_names> runid=<run_id>
LB	<sample_id>
SM	<barcode_name> (only if barcoding, and barcode is not "unclassified")
al	<barcode_alias> (only if barcoding, same as SM tag if no alias)

Read Tags

Tag	Description
RG:Z:	<runid>_<basecalling_model>_<barcode_arrangement>
qs:f:	mean basecall q-score
ts:i:	the number of samples trimmed from the start of the signal
ns:i:	the basecalled sequence corresponds to the interval signal[ts : ns] the move table maps to the same interval. note that ns reflects trimming (if any) from the rear of the signal.
mx:i:	read mux
ch:i:	read channel
rn:i:	read number
st:Z:	read start time (in UTC)
du:f:	duration of the read (in seconds)
fn:Z:	file name
sm:f:	scaling midpoint/mean/median (pA to ~0-mean/1-sd)
sd:f:	scaling dispersion (pA to ~0-mean/1-sd)
sv:Z:	scaling version
mv:B:c	sequence to signal move table (optional)
dx:i:	bool to signify duplex read (only in duplex mode)
pi:Z:	parent read id for a split read
sp:i:	start coordinate of split read in parent read signal
bh:i:	number of detected bedfile hits (only if alignment was performed with a specified bed-file)
MN:i:	Length of sequence at the time MM and ML were produced

Poly(A/T) Tags

When dorado is run with poly(A/T) estimation enabled, additional tags are added to each SAM record as follows:

• pt:i is the estimated poly(A/T) tail length in cDNA and dRNA reads
• pa:B:i is an array of signal positions related to the poly(A/T) estimation, in order:
  • The position in the signal used as the anchor for the poly(A/T) search
  • The start of the poly(A/T) region
  • The end of the poly(A/T) region
  • The the start of a secondary poly(A/T) region in the case of plasmids, (-1 otherwise or if not found)
  • The end of a secondary poly(A/T) region in the case of plasmids, (-1 otherwise or if not found)