Bismark Processing Report

Alignment

Sequence pairs analysed in total	10000000
Paired-end alignments with a unique best hit	803651
Pairs without alignments under any condition	8903803
Pairs that did not map uniquely	292546
Genomic sequence context not extractable (edges of chromosomes)	0

Cytosine Methylation

Total C's analysed	23154065
Methylated C's in CpG context	2018853
Methylated C's in CHG context	83895
Methylated C's in CHH context	571199
Methylated C's in Unknown context	6834
Unmethylated C's in CpG context	1311294
Unmethylated C's in CHG context	4958974
Unmethylated C's in CHH context	14209850
Unmethylated C's in Unknown context	78717
Percentage methylation (CpG context)	60.6%
Percentage methylation (CHG context)	1.7%
Percentage methylation (CHH context)	3.9%
Methylated C's in Unknown context	N/A%

Alignment to Individual Bisulfite Strands

OT	401517	original top strand
CTOT	0	complementary to original top strand
CTOB	0	complementary to original bottom strand
OB	402134	original bottom strand

Alignments analysed	1607302
Unique alignments	1576069
Duplicates removed	31233
Duplicated alignments were found at 26627 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_virginica/BSseq/cvir_bsseq_all_pe_R1.fastq.gz and /gscratch/scrubbed/samwhite/data/C_virginica/BSseq/cvir_bsseq_all_pe_R2.fastq.gz

Alignment

Cytosine Methylation

Alignment to Individual Bisulfite Strands

Deduplication

Cytosine Methylation after Extraction

Nucleotide Coverage

M-Bias Plot