Bismark report for: /gscratch/scrubbed/sr320/031520-TG-bs/Mcap_trim/Meth10_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031520-TG-bs/Mcap_trim/Meth10_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:	83382907
Number of paired-end alignments with a unique best hit:	33024348
Mapping efficiency:	39.6% 
Sequence pairs with no alignments under any condition:	35534143
Sequence pairs did not map uniquely:	14824416
Sequence pairs which were discarded because genomic sequence could not be extracted:	563

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	7768041	((converted) top strand)
GA/CT/CT:	8745272	(complementary to (converted) top strand)
GA/CT/GA:	8753450	(complementary to (converted) bottom strand)
CT/GA/GA:	7757022	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1475090477

Total methylated C's in CpG context:	29844699
Total methylated C's in CHG context:	3296608
Total methylated C's in CHH context:	11774846
Total methylated C's in Unknown context:	800724

Total unmethylated C's in CpG context:	217800127
Total unmethylated C's in CHG context:	258991853
Total unmethylated C's in CHH context:	953382344
Total unmethylated C's in Unknown context:	4438005

C methylated in CpG context:	12.1%
C methylated in CHG context:	1.3%
C methylated in CHH context:	1.2%
C methylated in unknown context (CN or CHN):	15.3%


Bismark completed in 0d 6h 9m 36s