Bismark report for: /gscratch/scrubbed/samwhite/data/P_generosa/BSeq/rrbs/pgen_bsseq_all_R1.fastq.gz (version: v0.19.0)
Option '--directional' specified (default mode): alignments to complementary strands (CTOT, CTOB) were ignored (i.e. not performed)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/scrubbed/samwhite/data/P_generosa/Pgenerosa_v071/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals

Final Alignment report
======================
Sequences analysed in total:	10000000
Number of alignments with a unique best hit from the different alignments:	5392088
Mapping efficiency:	53.9%
Sequences with no alignments under any condition:	2893485
Sequences did not map uniquely:	1714427
Sequences which were discarded because genomic sequence could not be extracted:	37064

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	2705305	((converted) top strand)
CT/GA:	2649719	((converted) bottom strand)
GA/CT:	0	(complementary to (converted) top strand)
GA/GA:	0	(complementary to (converted) bottom strand)

Number of alignments to (merely theoretical) complementary strands being rejected in total:	0

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	85972609

Total methylated C's in CpG context:	2840905
Total methylated C's in CHG context:	452489
Total methylated C's in CHH context:	778216
Total methylated C's in Unknown context:	15821

Total unmethylated C's in CpG context:	9613477
Total unmethylated C's in CHG context:	17605608
Total unmethylated C's in CHH context:	54681914
Total unmethylated C's in Unknown context:	208382

C methylated in CpG context:	22.8%
C methylated in CHG context:	2.5%
C methylated in CHH context:	1.4%
C methylated in Unknown context (CN or CHN):	7.1%


Bismark completed in 0d 1h 7m 3s