Bismark report for: ERR12308525_val_1.fq.gz and ERR12308525_val_2.fq.gz (version: v0.24.2)
Bismark was run with Bowtie 2 against the bisulfite genome of /mmfs1/gscratch/scrubbed/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:	86241924
Number of paired-end alignments with a unique best hit:	30136136
Mapping efficiency:	34.9% 
Sequence pairs with no alignments under any condition:	46119674
Sequence pairs did not map uniquely:	9986114
Sequence pairs which were discarded because genomic sequence could not be extracted:	16

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	15060889	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	15075231	((converted) bottom strand)

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

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1697176669

Total methylated C's in CpG context:	56436562
Total methylated C's in CHG context:	11142854
Total methylated C's in CHH context:	27550209
Total methylated C's in Unknown context:	245339

Total unmethylated C's in CpG context:	192491672
Total unmethylated C's in CHG context:	312564717
Total unmethylated C's in CHH context:	1096990655
Total unmethylated C's in Unknown context:	6790986

C methylated in CpG context:	22.7%
C methylated in CHG context:	3.4%
C methylated in CHH context:	2.4%
C methylated in Unknown context (CN or CHN):	3.5%


Bismark completed in 0d 4h 18m 50s