Bismark report for: /gscratch/srlab/strigg/data/Pgenr/FASTQS/2019_broodstock_amb_v_lowpH/Tank3-15-16_R1_001.fastq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/2019_broodstock_amb_v_lowpH/Tank3-15-16_R2_001.fastq.gz (version: v0.19.0)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Pgenr/Pgenr_070_10K/ with the specified options: -q --score-min L,0,-1.2 -p 28 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --minins 60 --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:	49500297
Number of paired-end alignments with a unique best hit:	32703150
Mapping efficiency:	66.1% 
Sequence pairs with no alignments under any condition:	12520575
Sequence pairs did not map uniquely:	4276572
Sequence pairs which were discarded because genomic sequence could not be extracted:	43010

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	16319185	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	16340955	((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:	1543256364

Total methylated C's in CpG context:	34848485
Total methylated C's in CHG context:	9132359
Total methylated C's in CHH context:	36416222
Total methylated C's in Unknown context:	1963727


Total unmethylated C's in CpG context:	148295953
Total unmethylated C's in CHG context:	269602751
Total unmethylated C's in CHH context:	1044960594
Total unmethylated C's in Unknown context:	10300596


C methylated in CpG context:	19.0%
C methylated in CHG context:	3.3%
C methylated in CHH context:	3.4%
C methylated in unknown context (CN or CHN):	16.0%


Bismark completed in 0d 17h 28m 12s