Bismark report for: /gscratch/scrubbed/sr320/031520-TG-bs/Mcap_trim/Meth18_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Mcap_trim/Meth18_R2_001_val_2.fq.gz (version: v0.21.0)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/froger/Mcap_Genome/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500
Option '--non_directional' specified: alignments to all strands were being performed (OT, OB, CTOT, CTOB)

Final Alignment report
======================
Sequence pairs analysed in total:	61585400
Number of paired-end alignments with a unique best hit:	14001402
Mapping efficiency:	22.7% 
Sequence pairs with no alignments under any condition:	41193946
Sequence pairs did not map uniquely:	6390052
Sequence pairs which were discarded because genomic sequence could not be extracted:	221

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	3447824	((converted) top strand)
GA/CT/CT:	3561023	(complementary to (converted) top strand)
GA/CT/GA:	3549170	(complementary to (converted) bottom strand)
CT/GA/GA:	3443164	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	631032858

Total methylated C's in CpG context:	14510651
Total methylated C's in CHG context:	1426130
Total methylated C's in CHH context:	5563948
Total methylated C's in Unknown context:	437143

Total unmethylated C's in CpG context:	92393953
Total unmethylated C's in CHG context:	109898929
Total unmethylated C's in CHH context:	407239247
Total unmethylated C's in Unknown context:	1936782

C methylated in CpG context:	13.6%
C methylated in CHG context:	1.3%
C methylated in CHH context:	1.3%
C methylated in unknown context (CN or CHN):	18.4%


Bismark completed in 0d 3h 11m 57s