SAM Tags: XR, XG, XM (Bismark-compatible)

bwa-mem3 mem --meth emits three Bismark-compatible auxiliary tags on each output record: XR:Z, XG:Z, and XM:Z. These tags are read by bismark_methylation_extractor, deduplicate_bismark, methylKit processBismarkAln, methtuple, DMRfinder, epialleleR, MethylDackel, and biscuit’s per-read methylation tools.

Tag reference

XR:Z — read conversion direction

XR:Z records which conversion was applied to the read at FASTQ ingest:

• CT — C→T conversion applied; this is an R1 read or single-end read.
• GA — G→A conversion applied; this is an R2 read.

XG:Z — genome strand of the alignment

XG:Z indicates which doubled-reference strand the read aligned to:

• CT — read aligned to the C→T-projected forward strand (OT).
• GA — read aligned to the G→A-projected forward strand (OB).

For properly paired directional reads, R1 and R2 of a fragment naturally share XG:Z. Discordant pairs (already flagged with 0x200 by the chimera-QC heuristic) may see XG:Z diverge between mates.

XM:Z — methylation call string

Per-base methylation call. Each character corresponds to one SEQ base:

The string is in SEQ orientation (matches the BAM SEQ field): for reads with the 0x10 flag set, both SEQ and XM:Z are reverse-complemented relative to FASTQ-original orientation.

Computation

Under --meth, the doubled c2t reference (<prefix>.bwameth.c2t.*) is folded once at startup into an in-memory un-converted pac (the meth_orig_ref module — src/meth_orig_ref.cpp). The fold uses (f, r) → original recovery on every position via a 5-row table:

Per mapped record, meth_build_xm slices the un-converted forward-strand window at the read’s footprint plus 2 bp of context on either side, then walks the BAM CIGAR jointly over the restored SEQ and the ref window. The classifier matches Bismark’s methylation_call:

match position with ref[t] == 'C' (top strand) or 'G' (bottom strand):
    determine context from ref[t±1], ref[t±2]
        N in either context base    -> u/U (unknown context)
        ref[t±1] == G/C (per strand) -> z/Z (CpG)
        ref[t±2] == G/C (per strand) -> x/X (CHG)
        otherwise                    -> h/H (CHH)
    determine methylation:
        read base == C/G (per strand) -> uppercase (methylated)
        read base == T/A (per strand) -> lowercase (unmethylated)
        otherwise                      -> '.'
insertion / soft clip                  -> '.' per consumed read base
deletion / N op                         -> no XM emit
hard clip / pad                         -> no XM emit

The top vs bottom strand choice is driven by XG:Z (= cmap direction), not by the SAM 0x10 (RC) flag. CTOT reads (R2 mapped forward to a top-strand contig with 0x10 set) and OB reads (R1 mapped RC to a bottom-strand contig) are both handled by reading the rule table from the strand encoded in XG. The walk runs in SEQ orientation throughout — no RC of the ref slice or the read.

For bottom-strand methylation, the C of interest at forward position P is encoded as a G on the forward strand (complement of bottom-strand C). The downstream context on the bottom strand corresponds to upstream positions on the forward strand; the classifier indexes ref[t-1] and ref[t-2] instead of ref[t+1] and ref[t+2], and looks for a C (forward) instead of a G to flag CpG.

Inspecting tags with samtools

samtools view out.bam | head -1 | tr '\t' '\n' | grep -E '^X[RGM]:'

Expected output looks like:

XR:Z:CT
XG:Z:CT
XM:Z:..z..h..Z..x..h.....Z..

See also

• Overview
• Conversion details
• Chimera QC and header rewriting
• Flags: –set-as-failed, –chimera-qc
• User Guide → Output: SAM/BAM, headers, tags