Bismark Processing Report

Alignment

Sequence pairs analysed in total	27014996
Paired-end alignments with a unique best hit	13096503
Pairs without alignments under any condition	11583837
Pairs that did not map uniquely	2334656
Genomic sequence context not extractable (edges of chromosomes)	71210

Cytosine Methylation

Total C's analysed	408341472
Methylated C's in CpG context	12050369
Methylated C's in CHG context	1978703
Methylated C's in CHH context	4316329
Methylated C's in Unknown context	164999
Unmethylated C's in CpG context	45453808
Unmethylated C's in CHG context	84263168
Unmethylated C's in CHH context	260279095
Unmethylated C's in Unknown context	2736696
Percentage methylation (CpG context)	21.0%
Percentage methylation (CHG context)	2.3%
Percentage methylation (CHH context)	1.6%
Methylated C's in Unknown context	N/A%

Alignment to Individual Bisulfite Strands

OT	0	original top strand
CTOT	0	complementary to original top strand
CTOB	0	complementary to original bottom strand
OB	13025293	original bottom strand

Alignments analysed	13025293
Unique alignments	10532562
Duplicates removed	2492731
Duplicated alignments were found at 973800 different positions

Total C's analysed	236315921
Methylated C's in CpG context	7947047
Methylated C's in CHG context	1212866
Methylated C's in CHH context	2796994
Unmethylated C's in CpG context	24524456
Unmethylated C's in CHG context	47714057
Unmethylated C's in CHH context	152120501
Percentage methylation (CpG context)	24.5%
Percentage methylation (CHG context)	2.5%
Percentage methylation (CHH context)	1.8%

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/srlab/strigg/data/Pgenr/FASTQS/data_for_genome_comparison/EPI-111_S29_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/data_for_genome_comparison/EPI-111_S29_L005_R2_001_val_2.fq.gz

Alignment

Cytosine Methylation

Alignment to Individual Bisulfite Strands

Deduplication

Cytosine Methylation after Extraction

Nucleotide Coverage

M-Bias Plot