Bismark Processing Report

Alignment

Sequence pairs analysed in total	5000000
Paired-end alignments with a unique best hit	2173514
Pairs without alignments under any condition	2418753
Pairs that did not map uniquely	407733
Genomic sequence context not extractable (edges of chromosomes)	183

Cytosine Methylation

Total C's analysed	42833940
Methylated C's in CpG context	760506
Methylated C's in CHG context	20354
Methylated C's in CHH context	72398
Methylated C's in Unknown context	5702
Unmethylated C's in CpG context	4201008
Unmethylated C's in CHG context	6972501
Unmethylated C's in CHH context	30807173
Unmethylated C's in Unknown context	83877
Percentage methylation (CpG context)	15.3%
Percentage methylation (CHG context)	0.3%
Percentage methylation (CHH context)	0.2%
Methylated C's in Unknown context	N/A%

Alignment to Individual Bisulfite Strands

OT	1091934	original top strand
CTOT	0	complementary to original top strand
CTOB	0	complementary to original bottom strand
OB	1081397	original bottom strand

Alignments analysed	4346662
Unique alignments	4203184
Duplicates removed	143478
Duplicated alignments were found at 85854 different positions

Total C's analysed	{{total_C_count_splitting}}
Methylated C's in CpG context	{{meth_CpG_splitting}}
Methylated C's in CHG context	{{meth_CHG_splitting}}
Methylated C's in CHH context	{{meth_CHH_splitting}}
Unmethylated C's in CpG context	{{unmeth_CpG_splitting}}
Unmethylated C's in CHG context	{{unmeth_CHG_splitting}}
Unmethylated C's in CHH context	{{unmeth_CHH_splitting}}
Percentage methylation (CpG context)	{{perc_CpG_splitting}}%
Percentage methylation (CHG context)	{{perc_CHG_splitting}}%
Percentage methylation (CHH context)	{{perc_CHH_splitting}}%

Nucleotide Coverage

Nucleotide Class	Counts Sample	Counts Genome	% in Sample	% in Genome	fold coverage
A	{{nuc_A_counts_obs}}	{{nuc_A_counts_exp}}	{{nuc_A_p_obs}}	{{nuc_A_p_exp}}	{{nuc_A_coverage}}
T	{{nuc_T_counts_obs}}	{{nuc_T_counts_exp}}	{{nuc_T_p_obs}}	{{nuc_T_p_exp}}	{{nuc_T_coverage}}
C	{{nuc_C_counts_obs}}	{{nuc_C_counts_exp}}	{{nuc_C_p_obs}}	{{nuc_C_p_exp}}	{{nuc_C_coverage}}
G	{{nuc_G_counts_obs}}	{{nuc_G_counts_exp}}	{{nuc_G_p_obs}}	{{nuc_G_p_exp}}	{{nuc_G_coverage}}
AC	{{nuc_AC_counts_obs}}	{{nuc_AC_counts_exp}}	{{nuc_AC_p_obs}}	{{nuc_AC_p_exp}}	{{nuc_AC_coverage}}
CA	{{nuc_CA_counts_obs}}	{{nuc_CA_counts_exp}}	{{nuc_CA_p_obs}}	{{nuc_CA_p_exp}}	{{nuc_CA_coverage}}
TC	{{nuc_TC_counts_obs}}	{{nuc_TC_counts_exp}}	{{nuc_TC_p_obs}}	{{nuc_TC_p_exp}}	{{nuc_TC_coverage}}
CT	{{nuc_CT_counts_obs}}	{{nuc_CT_counts_exp}}	{{nuc_CT_p_obs}}	{{nuc_CT_p_exp}}	{{nuc_CT_coverage}}
CC	{{nuc_CC_counts_obs}}	{{nuc_CC_counts_exp}}	{{nuc_CC_p_obs}}	{{nuc_CC_p_exp}}	{{nuc_CC_coverage}}
CG	{{nuc_CG_counts_obs}}	{{nuc_CG_counts_exp}}	{{nuc_CG_p_obs}}	{{nuc_CG_p_exp}}	{{nuc_CG_coverage}}
GC	{{nuc_GC_counts_obs}}	{{nuc_GC_counts_exp}}	{{nuc_GC_p_obs}}	{{nuc_GC_p_exp}}	{{nuc_GC_coverage}}
GG	{{nuc_GG_counts_obs}}	{{nuc_GG_counts_exp}}	{{nuc_GG_p_obs}}	{{nuc_GG_p_exp}}	{{nuc_GG_coverage}}
AG	{{nuc_AG_counts_obs}}	{{nuc_AG_counts_exp}}	{{nuc_AG_p_obs}}	{{nuc_AG_p_exp}}	{{nuc_AG_coverage}}
GA	{{nuc_GA_counts_obs}}	{{nuc_GA_counts_exp}}	{{nuc_GA_p_obs}}	{{nuc_GA_p_exp}}	{{nuc_GA_coverage}}
TG	{{nuc_TG_counts_obs}}	{{nuc_TG_counts_exp}}	{{nuc_TG_p_obs}}	{{nuc_TG_p_exp}}	{{nuc_TG_coverage}}
GT	{{nuc_GT_counts_obs}}	{{nuc_GT_counts_exp}}	{{nuc_GT_p_obs}}	{{nuc_GT_p_exp}}	{{nuc_GT_coverage}}
TT	{{nuc_TT_counts_obs}}	{{nuc_TT_counts_exp}}	{{nuc_TT_p_obs}}	{{nuc_TT_p_exp}}	{{nuc_TT_coverage}}
TA	{{nuc_TA_counts_obs}}	{{nuc_TA_counts_exp}}	{{nuc_TA_p_obs}}	{{nuc_TA_p_exp}}	{{nuc_TA_coverage}}
AT	{{nuc_AT_counts_obs}}	{{nuc_AT_counts_exp}}	{{nuc_AT_p_obs}}	{{nuc_AT_p_exp}}	{{nuc_AT_coverage}}
AA	{{nuc_AA_counts_obs}}	{{nuc_AA_counts_exp}}	{{nuc_AA_p_obs}}	{{nuc_AA_p_exp}}	{{nuc_AA_coverage}}

/gscratch/scrubbed/samwhite/data/C_gigas/BSseq/cgig_bsseq_pe_all_R1.fastq.gz and /gscratch/scrubbed/samwhite/data/C_gigas/BSseq/cgig_bsseq_pe_all_R2.fastq.gz

Alignment

Cytosine Methylation

Alignment to Individual Bisulfite Strands

Deduplication

Cytosine Methylation after Extraction

Nucleotide Coverage

M-Bias Plot