Bismark report for: /mmfs1/gscratch/coenv/sr320/cod-bs/03B_1.fastq.gz and /mmfs1/gscratch/coenv/sr320/cod-bs/03B_2.fastq.gz (version: v0.24.2)
Bismark was run with Bowtie 2 against the bisulfite genome of /mmfs1/gscratch/scrubbed/sr320/github/project-cod-temperature/data/genome/ with the specified options: -q --score-min L,0,-0.8 -p 8 --reorder --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:	52740330
Number of paired-end alignments with a unique best hit:	37055762
Mapping efficiency:	70.3% 
Sequence pairs with no alignments under any condition:	10545459
Sequence pairs did not map uniquely:	5139109
Sequence pairs which were discarded because genomic sequence could not be extracted:	62

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	18497701	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	18557999	((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:	2348843863

Total methylated C's in CpG context:	244927516
Total methylated C's in CHG context:	15312678
Total methylated C's in CHH context:	53564039
Total methylated C's in Unknown context:	4756331

Total unmethylated C's in CpG context:	87259909
Total unmethylated C's in CHG context:	466272303
Total unmethylated C's in CHH context:	1481507418
Total unmethylated C's in Unknown context:	7775025

C methylated in CpG context:	73.7%
C methylated in CHG context:	3.2%
C methylated in CHH context:	3.5%
C methylated in Unknown context (CN or CHN):	38.0%


Bismark completed in 0d 3h 53m 34s