Bismark Processing Report

Alignment

Sequence pairs analysed in total	1000000
Paired-end alignments with a unique best hit	518103
Pairs without alignments under any condition	286502
Pairs that did not map uniquely	195395
Genomic sequence context not extractable (edges of chromosomes)	0

Cytosine Methylation

Total C's analysed	13806945
Methylated C's in CpG context	1263772
Methylated C's in CHG context	78374
Methylated C's in CHH context	384212
Methylated C's in Unknown context	36797
Unmethylated C's in CpG context	483667
Unmethylated C's in CHG context	2916755
Unmethylated C's in CHH context	8680165
Unmethylated C's in Unknown context	171742
Percentage methylation (CpG context)	72.3%
Percentage methylation (CHG context)	2.6%
Percentage methylation (CHH context)	4.2%
Methylated C's in Unknown context	N/A%

Alignment to Individual Bisulfite Strands

OT	131416	original top strand
CTOT	127670	complementary to original top strand
CTOB	127990	complementary to original bottom strand
OB	131027	original bottom strand

Alignments analysed	518103
Unique alignments	517334
Duplicates removed	769
Duplicated alignments were found at 751 different positions

Total C's analysed	9248047
Methylated C's in CpG context	833778
Methylated C's in CHG context	54322
Methylated C's in CHH context	246563
Unmethylated C's in CpG context	327574
Unmethylated C's in CHG context	1940270
Unmethylated C's in CHH context	5845540
Percentage methylation (CpG context)	71.8%
Percentage methylation (CHG context)	2.7%
Percentage methylation (CHH context)	4.0%

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}}

zr2096_7_s1_R1_val_1.fq.gz and zr2096_7_s1_R2_val_2.fq.gz

Alignment

Cytosine Methylation

Alignment to Individual Bisulfite Strands

Deduplication

Cytosine Methylation after Extraction

Nucleotide Coverage

M-Bias Plot