Bismark report for: /gscratch/scrubbed/sr320/031320-TG-bs/Meth13_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031320-TG-bs/Meth13_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:	10000000
Number of paired-end alignments with a unique best hit:	5475520
Mapping efficiency:	54.8% 
Sequence pairs with no alignments under any condition:	1638801
Sequence pairs did not map uniquely:	2885679
Sequence pairs which were discarded because genomic sequence could not be extracted:	53

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	1341380	((converted) top strand)
GA/CT/CT:	1400437	(complementary to (converted) top strand)
GA/CT/GA:	1397608	(complementary to (converted) bottom strand)
CT/GA/GA:	1336042	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	271145115

Total methylated C's in CpG context:	3612158
Total methylated C's in CHG context:	353248
Total methylated C's in CHH context:	1023680
Total methylated C's in Unknown context:	8911

Total unmethylated C's in CpG context:	52926601
Total unmethylated C's in CHG context:	49943382
Total unmethylated C's in CHH context:	163286046
Total unmethylated C's in Unknown context:	289268

C methylated in CpG context:	6.4%
C methylated in CHG context:	0.7%
C methylated in CHH context:	0.6%
C methylated in unknown context (CN or CHN):	3.0%


Bismark completed in 0d 0h 44m 3s