Bismark report for: /gscratch/scrubbed/yaamini/data/Gigas-WGBS/2019-09-03-Trimmed-Files/YRVA_R1_001.fastq.gz and /gscratch/scrubbed/yaamini/data/Gigas-WGBS/2019-09-03-Trimmed-Files/YRVA_R2_001.fastq.gz (version: v0.21.0)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/scrubbed/yaamini/data/Gigas-WGBS/2019-09-03-Bismark-Inputs/Crassostrea_gigas.oyster_v9.dna_sm.toplevel/ with the specified options: -q --score-min L,0,-0.9 -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:	67542867
Number of paired-end alignments with a unique best hit:	43217945
Mapping efficiency:	64.0% 
Sequence pairs with no alignments under any condition:	19815721
Sequence pairs did not map uniquely:	4509201
Sequence pairs which were discarded because genomic sequence could not be extracted:	15910

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	21607927	((converted) top strand)
GA/CT/CT:	16626	(complementary to (converted) top strand)
GA/CT/GA:	17271	(complementary to (converted) bottom strand)
CT/GA/GA:	21560211	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2014476985

Total methylated C's in CpG context:	38388669
Total methylated C's in CHG context:	12919248
Total methylated C's in CHH context:	61221106
Total methylated C's in Unknown context:	2748438

Total unmethylated C's in CpG context:	208388236
Total unmethylated C's in CHG context:	321769730
Total unmethylated C's in CHH context:	1371789996
Total unmethylated C's in Unknown context:	12474356

C methylated in CpG context:	15.6%
C methylated in CHG context:	3.9%
C methylated in CHH context:	4.3%
C methylated in unknown context (CN or CHN):	18.1%


Bismark completed in 0d 8h 33m 41s