Bismark Processing Report

Alignment

Sequence pairs analysed in total	31,847,541
Paired-end alignments with a unique best hit	16,108,088
Pairs without alignments under any condition	9,175,758
Pairs that did not map uniquely	6,563,695
Genomic sequence context not extractable (edges of chromosomes)	5

Cytosine Methylation

Total C's analysed	446,271,830
Methylated C's in CpG context	48,190,808
Methylated C's in CHG context	2,774,831
Methylated C's in CHH context	12,251,657
Methylated C's in Unknown context	1,258,835
Unmethylated C's in CpG context	14,405,999
Unmethylated C's in CHG context	95,964,094
Unmethylated C's in CHH context	272,684,441
Unmethylated C's in Unknown context	5,548,505
Percentage methylation (CpG context)	77.0%
Percentage methylation (CHG context)	2.8%
Percentage methylation (CHH context)	4.3%
Methylated C's in Unknown context	N/A%

Alignment to Individual Bisulfite Strands

OT	4,345,578	original top strand
CTOT	3,702,815	complementary to original top strand
CTOB	3,705,364	complementary to original bottom strand
OB	4,354,326	original bottom strand

Deduplication

Alignments analysed	16,108,083
Unique alignments	14,083,414
Duplicates removed	2,024,669
Duplicated alignments were found at 1660011 different positions

Cytosine Methylation after Extraction

Total C's analysed	255,572,824
Methylated C's in CpG context	26,756,008
Methylated C's in CHG context	1,647,018
Methylated C's in CHH context	7,002,283
Unmethylated C's in CpG context	8,438,242
Unmethylated C's in CHG context	54,139,076
Unmethylated C's in CHH context	157,590,197
Percentage methylation (CpG context)	76.0%
Percentage methylation (CHG context)	3.0%
Percentage methylation (CHH context)	4.3%

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/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_9_s1_R1_val_1.fq.gz and /gscratch/scrubbed/yaamini/data/Virginica-MBD/2018-10-17-Trimmed-Files//zr2096_9_s1_R2_val_2.fq.gz

Alignment

Cytosine Methylation

Alignment to Individual Bisulfite Strands

Deduplication

Cytosine Methylation after Extraction

Nucleotide Coverage

M-Bias Plot