Failed replicate the lambda alignment from the graphmap publication

[Shengpei-Luke-Chen]

Hi GraphMap team,

Currently, I am exploring options for ONT reads mapping for my company.
I am very impressed by GraphMap's performance, and the article is very helpful.
So thank you for all the amazing work.

What I am stuck right now is replicating the lambda aligning from GraphMap's publication. My mapped bases (coverage) of lambda reads is very different from the article.

Dataset: Directly download from the ref-12. Both the 1d and 2d data. It would be about 4,500X coverage.
Lambda reference: Same with the article. NC_001416 from NCBI
GraphMap version: v0.5.2
Alignment command line: As the article states, all default.
graphmap align -r NC_001416.fasta -d 1d.fastq -o 1d.graphmap.sam
graphmap align -r NC_001416.fasta -d 2d.fastq -o 2d.graphmap.sam
Mapped base/coverage calculation: Since the article did not states how the mapped base or coverage was calculated, I just simply use samtools stats without any filter.

Symptom: My coverage is way lower than the article.

• Article (specifically, Figure 3b and Supplementary Table-s3):
  • % bases mapped = 68.1%
  • Avg. Coverage = 2552.8
• My result (detail samtools stats attached):
  • 1d reads:
    • % bases mapped = 65,689,800/155,370,698 = 42.28%
    • Avg. Coverage = 65,689,800/48,502 = 1354.37
  • 2d reads:
    • % bases mapped = 12,783,088/55,854,289 = 22.89%
    • Avg. Coverage = 12,783,088/48,502 = 263.56

Please let me know if you need me to provide more information.
Thank you ahead.
Luke

1d.graphmap.status.txt

raw total sequences:	29458
filtered sequences:	0
sequences:	29458
is sorted:	0
1st fragments:	29458
last fragments:	0
reads mapped:	11843
reads mapped and paired:	0	# paired-end technology bit set + both mates mapped
reads unmapped:	17615
reads properly paired:	0	# proper-pair bit set
reads paired:	0	# paired-end technology bit set
reads duplicated:	0	# PCR or optical duplicate bit set
reads MQ0:	0	# mapped and MQ=0
reads QC failed:	0
non-primary alignments:	0
total length:	155370698	# ignores clipping
total first fragment length:	155370698	# ignores clipping
total last fragment length:	0	# ignores clipping
bases mapped:	65689800	# ignores clipping
bases mapped (cigar):	65139719	# more accurate
bases trimmed:	0
bases duplicated:	0
mismatches:	32663756	# from NM fields
error rate:	5.014415e-01	# mismatches / bases mapped (cigar)
average length:	5274
average first fragment length:	5274
average last fragment length:	0
maximum length:	110057
maximum first fragment length:	0
maximum last fragment length:	0
average quality:	4.1
insert size average:	0.0
insert size standard deviation:	0.0
inward oriented pairs:	0
outward oriented pairs:	0
pairs with other orientation:	0
pairs on different chromosomes:	0
percentage of properly paired reads (%):	0.0

2d.graphmap.status.txt

raw total sequences:	11094
filtered sequences:	0
sequences:	11094
is sorted:	0
1st fragments:	11094
last fragments:	0
reads mapped:	2227
reads mapped and paired:	0	# paired-end technology bit set + both mates mapped
reads unmapped:	8867
reads properly paired:	0	# proper-pair bit set
reads paired:	0	# paired-end technology bit set
reads duplicated:	0	# PCR or optical duplicate bit set
reads MQ0:	0	# mapped and MQ=0
reads QC failed:	0
non-primary alignments:	0
total length:	55854289	# ignores clipping
total first fragment length:	55854289	# ignores clipping
total last fragment length:	0	# ignores clipping
bases mapped:	12783088	# ignores clipping
bases mapped (cigar):	12017411	# more accurate
bases trimmed:	0
bases duplicated:	0
mismatches:	5832782	# from NM fields
error rate:	4.853610e-01	# mismatches / bases mapped (cigar)
average length:	5034
average first fragment length:	5035
average last fragment length:	0
maximum length:	21158
maximum first fragment length:	0
maximum last fragment length:	0
average quality:	7.1
insert size average:	0.0
insert size standard deviation:	0.0
inward oriented pairs:	0
outward oriented pairs:	0
pairs with other orientation:	0
pairs on different chromosomes:	0
percentage of properly paired reads (%):	0.0