| Tag | Description | Is phred | Written by default |
|---|---|---|---|
| A2 | Read2Clipped3primeBasesKmer | No | No |
| AE | AssingedExons | No | No |
| AI | AssignedIntrons | No | No |
| AQ | Read2Clipped3primeBasesKmerQuality | Yes | No |
| AS | alignmentScore | No | No |
| BC | barcode | No | No |
| BD | gatk_insert_deletion_base_qualities | No | No |
| BI | gatk_insert_deletion_base_qualities | No | No |
| BK | isBulk | No | No |
| BX | umiCorrected | No | No |
| BZ | umiCorrectedQuality | Yes | No |
| CB | cellBarcode | No | No |
| CN | controlNumber | No | No |
| CX | clusterXpos | No | No |
| CY | clusterYpos | No | No |
| Cm | modified3BPContexts | No | No |
| Cu | unmodified3BPContexts | No | No |
| DA | allele | No | No |
| DS | siteCoordinate | No | No |
| DT | sourceType | No | No |
| E2 | Read1Clipped5primeBasesKmerQuality | Yes | No |
| EB | Read2Clipped5primeCycle | No | No |
| EQ | Read2Clipped5primeBasesKmerQuality | Yes | No |
| ES | EnzymeSequence | No | No |
| EX | exons | No | No |
| EX | experiment | No | No |
| Fc | flowCellId | No | No |
| Fi | filterFlag | No | No |
| GN | genes | No | No |
| H0 | HexamerSequenceR1 | No | No |
| H1 | HexamerPhredScoreR1 | Yes | No |
| H2 | HexamerSequenceR2 | No | No |
| H3 | HexamerPhredScoreR2 | Yes | No |
| HI | queryHitIndex | No | No |
| IN | introns | No | No |
| IS | ispcrSequence | No | No |
| IT | is_transcriptome | No | No |
| Is | instrument | No | No |
| JN | junctions | No | No |
| LI | ligationMotif | No | No |
| LY | sequencingLibrary | No | No |
| La | lane | No | No |
| MC | methylatedBaseCountForFragment | No | No |
| MD | alignment | No | No |
| MI | molecularIdentifier | No | No |
| MX | demultiplexingStrategy | No | No |
| NH | occurencesOfFragment | No | No |
| NM | editDistanceToReference | No | No |
| QM | molecularIdentifierQuality | Yes | No |
| QT | sampleBarcodeQuality | Yes | No |
| QX | barcodeQual | Yes | No |
| Qm | modified4BPContexts | No | No |
| Qu | unmodified4BPContexts | No | No |
| RC | moleculeOverseqCountIndex | No | No |
| RG | readGroup | No | No |
| RN | runNumber | No | No |
| RP | readPairNumber | No | Yes |
| RQ | umiQual | Yes | No |
| RR | rejectionReason | No | No |
| RS | recognizedStrand | No | No |
| RX | umi | No | No |
| RZ | recognizedSequence | No | No |
| SD | scarDescription | No | No |
| SM | sampleName | No | No |
| SP | IsSpliced | No | No |
| SQ | meanBaseQuality | No | No |
| TF | totalAssociatedFragmentsIncludingOverlflow | No | No |
| TR | totalRTreactions | No | No |
| TR | totalRTreactions | No | No |
| Ti | tile | No | No |
| Us | undigestedSiteCount | No | No |
| XA | alternativeAlignmentHits | No | No |
| XC | plateCoord | No | No |
| XM | perBaseMethylationStatus | No | No |
| XS | assignmentStatus | No | No |
| a1 | Read1Clipped3primeBasesKmer | No | No |
| aA | correctedIlluminaIndexSequence | No | No |
| aI | indexSequence | No | No |
| aQ | Read1Clipped3primeBasesKmerQuality | Yes | No |
| aa | rawIlluminaIndexSequence | No | No |
| af | associatedFragmentCount | No | No |
| af | totalAssociatedFragmentsInBam | No | No |
| ah | hammingDistanceToIndex | No | No |
| ap | phasedAllelicSNVs | No | No |
| au | phasednUnknownAllelicOriginSNVs | No | No |
| bc | rawBarcode | No | No |
| bi | barcodeIndex | No | No |
| dt | assingedDataType | No | No |
| e1 | Read1Clipped5primeBasesKmer | No | No |
| eB | Read1Clipped5primeCycle | No | No |
| eH | ExonHits amount of bases aligned to exon | No | No |
| eQ | Read2Clipped5primeBasesKmer | No | No |
| eq | EnzymeSequenceQualities | Yes | No |
| fS | fragmentSizeTag | No | No |
| fe | fragmentEndTag | No | No |
| fs | fragmentStartTag | No | No |
| hd | hammingDistanceRawBcAssignedBc | No | No |
| iH | IntronHits amount of bases aligned to intron | No | No |
| is | ispcrSequenceQualities | Yes | No |
| lh | ligationOverhangSequence | No | No |
| lq | ligationOverhangQuality | Yes | No |
| nM | editDistanceToReference | No | No |
| rP | randomPrimerStart | No | No |
| rS | randomPrimerSequence | No | No |
| rd | rtDuplicateIndex | No | No |
| rt | rtReactionIndex | No | No |
| sH | Total CHH methylated | No | No |
| sX | Total CHG methylated | No | No |
| sZ | Total CPG methylated | No | No |
| sh | Total CHH unmethylated | No | No |
| sx | Total CHG unmethylated | No | No |
| sz | Total CPG unmethylated | No | No |
| tu | second_umi | No | No |
| uC | totalUnmethylated | No | No |
| uL | umiLength | No | No |