Bismark report for: ERR12308522_val_1.fq.gz and ERR12308522_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:	84026603
Number of paired-end alignments with a unique best hit:	21731805
Mapping efficiency:	25.9% 
Sequence pairs with no alignments under any condition:	51543723
Sequence pairs did not map uniquely:	10751075
Sequence pairs which were discarded because genomic sequence could not be extracted:	5

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	10863770	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	10868030	((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:	1109717645

Total methylated C's in CpG context:	25020816
Total methylated C's in CHG context:	7274108
Total methylated C's in CHH context:	21600562
Total methylated C's in Unknown context:	316723

Total unmethylated C's in CpG context:	120647227
Total unmethylated C's in CHG context:	178070272
Total unmethylated C's in CHH context:	757104660
Total unmethylated C's in Unknown context:	6653943

C methylated in CpG context:	17.2%
C methylated in CHG context:	3.9%
C methylated in CHH context:	2.8%
C methylated in Unknown context (CN or CHN):	4.5%


Bismark completed in 0d 7h 8m 7s