Bismark report for: /gscratch/scrubbed/strigg/analyses/20200612/16C_32psu_3_S3_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/analyses/20200612/16C_32psu_3_S3_R2_001_val_2.fq.gz (version: v0.22.3)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/ with the specified options: -q --score-min L,0,-0.3 -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:	27011985
Number of paired-end alignments with a unique best hit:	11217924
Mapping efficiency:	41.5% 
Sequence pairs with no alignments under any condition:	9859755
Sequence pairs did not map uniquely:	5934306
Sequence pairs which were discarded because genomic sequence could not be extracted:	3

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	3013117	((converted) top strand)
GA/CT/CT:	2579738	(complementary to (converted) top strand)
GA/CT/GA:	2596089	(complementary to (converted) bottom strand)
CT/GA/GA:	3028977	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	387314162

Total methylated C's in CpG context:	30083711
Total methylated C's in CHG context:	690782
Total methylated C's in CHH context:	3807159
Total methylated C's in Unknown context:	76938

Total unmethylated C's in CpG context:	8849266
Total unmethylated C's in CHG context:	97921890
Total unmethylated C's in CHH context:	245961354
Total unmethylated C's in Unknown context:	304204

C methylated in CpG context:	77.3%
C methylated in CHG context:	0.7%
C methylated in CHH context:	1.5%
C methylated in unknown context (CN or CHN):	20.2%


Bismark completed in 0d 1h 32m 5s