Bismark Processing Report

Alignment

Sequence pairs analysed in total	10000
Paired-end alignments with a unique best hit	5173
Pairs without alignments under any condition	2846
Pairs that did not map uniquely	1981
Genomic sequence context not extractable (edges of chromosomes)	0

Cytosine Methylation

Total C's analysed	135136
Methylated C's in CpG context	11561
Methylated C's in CHG context	757
Methylated C's in CHH context	3769
Methylated C's in Unknown context	381
Unmethylated C's in CpG context	5280
Unmethylated C's in CHG context	27635
Unmethylated C's in CHH context	86134
Unmethylated C's in Unknown context	1740
Percentage methylation (CpG context)	68.6%
Percentage methylation (CHG context)	2.7%
Percentage methylation (CHH context)	4.2%
Methylated C's in Unknown context	N/A%

Alignment to Individual Bisulfite Strands

OT	1303	original top strand
CTOT	1304	complementary to original top strand
CTOB	1251	complementary to original bottom strand
OB	1315	original bottom strand

Alignments analysed	5173
Unique alignments	5173
Duplicates removed	0
Duplicated alignments were found at 0 different positions

Total C's analysed	88261
Methylated C's in CpG context	7407
Methylated C's in CHG context	500
Methylated C's in CHH context	2394
Unmethylated C's in CpG context	3462
Unmethylated C's in CHG context	17842
Unmethylated C's in CHH context	56656
Percentage methylation (CpG context)	68.1%
Percentage methylation (CHG context)	2.7%
Percentage methylation (CHH context)	4.1%

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}}

/Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_5_s1_R1_val_1.fq.gz and /Volumes/web/Athaliana/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_5_s1_R2_val_2.fq.gz

Alignment

Cytosine Methylation

Alignment to Individual Bisulfite Strands

Deduplication

Cytosine Methylation after Extraction

Nucleotide Coverage

M-Bias Plot