Bismark report for: SRR546472_val_1.fq.gz and SRR546472_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:	67603212
Number of paired-end alignments with a unique best hit:	38591038
Mapping efficiency:	57.1% 
Sequence pairs with no alignments under any condition:	19264242
Sequence pairs did not map uniquely:	9747932
Sequence pairs which were discarded because genomic sequence could not be extracted:	8

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	19280123	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	19310907	((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:	1111132155

Total methylated C's in CpG context:	15190491
Total methylated C's in CHG context:	938643
Total methylated C's in CHH context:	3575331
Total methylated C's in Unknown context:	26115

Total unmethylated C's in CpG context:	126068858
Total unmethylated C's in CHG context:	194670823
Total unmethylated C's in CHH context:	770688009
Total unmethylated C's in Unknown context:	2502993

C methylated in CpG context:	10.8%
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 6h 55m 34s