Bismark report for: SRR546473_val_1.fq.gz and SRR546473_val_2.fq.gz (version: v0.24.2)
Bismark was run with Bowtie 2 against the bisulfite genome of /home/shared/8TB_HDD_03/sr320/whale/reference/GCF_963853765.1/bismark_genome/ with the specified options: -q --score-min L,0,-0.6 --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500
Option '--directional' specified (default mode): alignments to complementary strands (CTOT, CTOB) were ignored (i.e. not performed)

Final Alignment report
======================
Sequence pairs analysed in total:	78285679
Number of paired-end alignments with a unique best hit:	43063897
Mapping efficiency:	55.0% 
Sequence pairs with no alignments under any condition:	23703946
Sequence pairs did not map uniquely:	11517836
Sequence pairs which were discarded because genomic sequence could not be extracted:	9

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	21503154	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	21560734	((converted) bottom strand)

Number of alignments to (merely theoretical) complementary strands being rejected in total:	0

Final Cytosine Methylation Report
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Total number of C's analysed:	1237797490

Total methylated C's in CpG context:	16717375
Total methylated C's in CHG context:	1046785
Total methylated C's in CHH context:	3981030
Total methylated C's in Unknown context:	29419

Total unmethylated C's in CpG context:	140045864
Total unmethylated C's in CHG context:	217565990
Total unmethylated C's in CHH context:	858440446
Total unmethylated C's in Unknown context:	2815395

C methylated in CpG context:	10.7%
C methylated in CHG context:	0.5%
C methylated in CHH context:	0.5%
C methylated in Unknown context (CN or CHN):	1.0%


Bismark completed in 0d 7h 56m 28s