Bismark Processing Report

Alignment

Sequence pairs analysed in total	10000000
Paired-end alignments with a unique best hit	5047522
Pairs without alignments under any condition	4108088
Pairs that did not map uniquely	844390
Genomic sequence context not extractable (edges of chromosomes)	456

Cytosine Methylation

Total C's analysed	105307378
Methylated C's in CpG context	1947531
Methylated C's in CHG context	44570
Methylated C's in CHH context	155977
Methylated C's in Unknown context	10465
Unmethylated C's in CpG context	10236643
Unmethylated C's in CHG context	17172924
Unmethylated C's in CHH context	75749733
Unmethylated C's in Unknown context	206032
Percentage methylation (CpG context)	16.0%
Percentage methylation (CHG context)	0.3%
Percentage methylation (CHH context)	0.2%
Methylated C's in Unknown context	N/A%

Alignment to Individual Bisulfite Strands

OT	2528514	original top strand
CTOT	0	complementary to original top strand
CTOB	0	complementary to original bottom strand
OB	2518552	original bottom strand

Alignments analysed	10094132
Unique alignments	9764095
Duplicates removed	330037
Duplicated alignments were found at 234968 different positions

Total C's analysed	{{total_C_count_splitting}}
Methylated C's in CpG context	{{meth_CpG_splitting}}
Methylated C's in CHG context	{{meth_CHG_splitting}}
Methylated C's in CHH context	{{meth_CHH_splitting}}
Unmethylated C's in CpG context	{{unmeth_CpG_splitting}}
Unmethylated C's in CHG context	{{unmeth_CHG_splitting}}
Unmethylated C's in CHH context	{{unmeth_CHH_splitting}}
Percentage methylation (CpG context)	{{perc_CpG_splitting}}%
Percentage methylation (CHG context)	{{perc_CHG_splitting}}%
Percentage methylation (CHH context)	{{perc_CHH_splitting}}%

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/samwhite/data/C_gigas/BSseq/cgig_bsseq_pe_all_R1.fastq.gz and /gscratch/scrubbed/samwhite/data/C_gigas/BSseq/cgig_bsseq_pe_all_R2.fastq.gz

Alignment

Cytosine Methylation

Alignment to Individual Bisulfite Strands

Deduplication

Cytosine Methylation after Extraction

Nucleotide Coverage

M-Bias Plot