Bismark Processing Report

Alignment

Sequence pairs analysed in total	36162144
Paired-end alignments with a unique best hit	17710187
Pairs without alignments under any condition	12311702
Pairs that did not map uniquely	6140255
Genomic sequence context not extractable (edges of chromosomes)	2042

Cytosine Methylation

Total C's analysed	772184400
Methylated C's in CpG context	56920247
Methylated C's in CHG context	2493970
Methylated C's in CHH context	12696299
Methylated C's in Unknown context	1006048
Unmethylated C's in CpG context	17366984
Unmethylated C's in CHG context	193472967
Unmethylated C's in CHH context	489233933
Unmethylated C's in Unknown context	2573007
Percentage methylation (CpG context)	76.6%
Percentage methylation (CHG context)	1.3%
Percentage methylation (CHH context)	2.5%
Methylated C's in Unknown context	N/A%

Alignment to Individual Bisulfite Strands

OT	4431790	original top strand
CTOT	4392273	complementary to original top strand
CTOB	4418297	complementary to original bottom strand
OB	4465785	original bottom strand

Alignments analysed	{{seqs_total_duplicates}}
Unique alignments	{{unique_alignments_duplicates}}
Duplicates removed	{{duplicate_alignments_duplicates}}
Duplicated alignments were found at {{different_positions_duplicates}} different positions

Total C's analysed	440070930
Methylated C's in CpG context	31719058
Methylated C's in CHG context	1431932
Methylated C's in CHH context	7345410
Unmethylated C's in CpG context	9758266
Unmethylated C's in CHG context	109733822
Unmethylated C's in CHH context	280082442
Percentage methylation (CpG context)	76.5%
Percentage methylation (CHG context)	1.3%
Percentage methylation (CHH context)	2.6%

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/strigg/TRIMG_adapt_5bp/TRIM_cat/8C_26psu_1_S9_R1_001_val_1.fq.gz and /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/8C_26psu_1_S9_R2_001_val_2.fq.gz

Alignment

Cytosine Methylation

Alignment to Individual Bisulfite Strands

Deduplication

Cytosine Methylation after Extraction

Nucleotide Coverage

M-Bias Plot