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_v073/ with the specified options: -q --score-min L,0,-0.6 -p 28 --reorder --ignore-quals

Final Alignment report
======================
Sequences analysed in total:	500000
Number of alignments with a unique best hit from the different alignments:	248421
Mapping efficiency:	49.7%
Sequences with no alignments under any condition:	173607
Sequences did not map uniquely:	77972
Sequences which were discarded because genomic sequence could not be extracted:	1867

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	124253	((converted) top strand)
CT/GA:	122301	((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:	3932963

Total methylated C's in CpG context:	133375
Total methylated C's in CHG context:	20534
Total methylated C's in CHH context:	36870
Total methylated C's in Unknown context:	773

Total unmethylated C's in CpG context:	438843
Total unmethylated C's in CHG context:	798954
Total unmethylated C's in CHH context:	2504387
Total unmethylated C's in Unknown context:	9063

C methylated in CpG context:	23.3%
C methylated in CHG context:	2.5%
C methylated in CHH context:	1.5%
C methylated in Unknown context (CN or CHN):	7.9%


Bismark completed in 0d 0h 3m 27s