Sequence identifiers containing both GRCh38 and CHM13 were found in the alignment of the GRCh38 reference genome

[yangyaxi4444]

When examining the BAM files generated from both GRCh38 and CHM13 mappings using vg giraffe, there's an unexpected presence of sequence headers from both reference genomes in each BAM file. For example:
In GRCh38-mapped BAM:
Copy@SQ SN:GRCh38#0#chr11 LN:135086622
@sq SN:GRCh38#0#chr10 LN:133797422
@sq SN:CHM13#0#chrY LN:26682553
@sq SN:CHM13#0#chrX LN:154259564
And similarly in CHM13-mapped BAM:

Headers contain sequences from both GRCh38 and CHM13
This occurs despite using separate reference graphs

would it influence and quantification step?

[yangyaxi4444]

hi, if anyone could help me with it

[glennhickey]

Which BAM file are you talking about? By default vg surject will use all reference paths, which include both GRCh38 and CHM13 in both graphs (chm13-referenecd and grch38-referened) unless otherwise specified.