Bismark Processing Report

Alignment

Sequence pairs analysed in total	16300374
Paired-end alignments with a unique best hit	8990034
Pairs without alignments under any condition	4456627
Pairs that did not map uniquely	2853713
Genomic sequence context not extractable (edges of chromosomes)	47414

Cytosine Methylation

Total C's analysed	273613473
Methylated C's in CpG context	9377073
Methylated C's in CHG context	1595448
Methylated C's in CHH context	8983360
Methylated C's in Unknown context	285276
Unmethylated C's in CpG context	30295668
Unmethylated C's in CHG context	57897191
Unmethylated C's in CHH context	165464733
Unmethylated C's in Unknown context	1344837
Percentage methylation (CpG context)	23.6%
Percentage methylation (CHG context)	2.7%
Percentage methylation (CHH context)	5.1%
Methylated C's in Unknown context	N/A%

Alignment to Individual Bisulfite Strands

OT	4435955	original top strand
CTOT	0	complementary to original top strand
CTOB	0	complementary to original bottom strand
OB	4506665	original bottom strand

Alignments analysed	8942620
Unique alignments	6264711
Duplicates removed	2677909
Duplicated alignments were found at 1500648 different positions

Total C's analysed	136529341
Methylated C's in CpG context	5133920
Methylated C's in CHG context	875886
Methylated C's in CHH context	5525110
Unmethylated C's in CpG context	13487431
Unmethylated C's in CHG context	28017758
Unmethylated C's in CHH context	83489236
Percentage methylation (CpG context)	27.6%
Percentage methylation (CHG context)	3.0%
Percentage methylation (CHH context)	6.2%

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/EPI-221_S33_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-221_S33_L004_R2_001_val_2.fq.gz

Alignment

Cytosine Methylation

Alignment to Individual Bisulfite Strands

Deduplication

Cytosine Methylation after Extraction

Nucleotide Coverage

M-Bias Plot