Bismark report for: /gscratch/scrubbed/sr320/031320-TG-bs/Meth18_R1_001_val_1.fq.gz and /gscratch/scrubbed/sr320/031320-TG-bs/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:	10000000
Number of paired-end alignments with a unique best hit:	2278352
Mapping efficiency:	22.8% 
Sequence pairs with no alignments under any condition:	6682550
Sequence pairs did not map uniquely:	1039098
Sequence pairs which were discarded because genomic sequence could not be extracted:	35

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	561403	((converted) top strand)
GA/CT/CT:	579475	(complementary to (converted) top strand)
GA/CT/GA:	577710	(complementary to (converted) bottom strand)
CT/GA/GA:	559729	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	102720230

Total methylated C's in CpG context:	2365050
Total methylated C's in CHG context:	233329
Total methylated C's in CHH context:	904159
Total methylated C's in Unknown context:	71651

Total unmethylated C's in CpG context:	15039802
Total unmethylated C's in CHG context:	17887150
Total unmethylated C's in CHH context:	66290740
Total unmethylated C's in Unknown context:	314958

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):	18.5%


Bismark completed in 0d 0h 23m 46s