Bismark

Bismark Processing Report

SRR5008109_WGBS_Seq_E14_d11_1_control_1_val_1.fq.gz and SRR5008109_WGBS_Seq_E14_d11_1_control_2_val_2.fq.gz

Data processed at 11:25 on 2018-08-16


Alignment Stats

Sequence pairs analysed in total 9399055
Paired-end alignments with a unique best hit 7018098
Pairs without alignments under any condition 1722286
Pairs that did not map uniquely 658671
Genomic sequence context not extractable (edges of chromosomes) 6
74.7%18.3%7.01%0.0000638%
Unique AlignmentsNo AlignmentMultiple AlignmentsNo Genomic Sequence

Cytosine Methylation

Total C's analysed 264469464
Methylated C's in CpG context 8364359
Methylated C's in CHG context 755431
Methylated C's in CHH context 2166832
Methylated C's in Unknown context 535
Unmethylated C's in CpG context 3380818
Unmethylated C's in CHG context 57592010
Unmethylated C's in CHH context 192210014
Unmethylated C's in Unknown context 56967
Percentage methylation (CpG context) 71.2%
Percentage methylation (CHG context) 1.3%
Percentage methylation (CHH context) 1.1%
Methylated C's in Unknown context N/A%
CpG contextCHG contextCHH context020406080100
% Methylation

Alignment to Individual Bisulfite Strands

OT 3544531 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 3473561 original bottom strand
OTCTOTCTOBOB00.5M1M1.5M2M2.5M3M3.5M
Number of Alignments

Deduplication

Alignments analysed 7018092
Unique alignments 6598101
Duplicates removed 419991
Duplicated alignments were found at 338524 different positions
94%5.98%
Unique AlignmentsDuplicate Alignments

Cytosine Methylation after Extraction

Total C's analysed 241956905
Methylated C's in CpG context 7173286
Methylated C's in CHG context 681193
Methylated C's in CHH context 1884937
Unmethylated C's in CpG context 2915868
Unmethylated C's in CHG context 52772247
Unmethylated C's in CHH context 176529374
Percentage methylation (CpG context) 71.1%
Percentage methylation (CHG context) 1.3%
Percentage methylation (CHH context) 1.1%
CpG contextCHH contextCHG context020406080100
% Methylation

M-Bias Plot

10203040506070809010002040608010000.2M0.4M0.6M0.8M1M
CpG methylationCHG methylationCHH methylationCpG total callsCHG total callsCHH total callsRead 1Position in Read [bp]% Methylation# Methylation Calls

10203040506070809002040608010000.2M0.4M0.6M0.8M1M
CpG methylationCHG methylationCHH methylationCpG total callsCHG total callsCHH total callsRead 2Position in read [bp]% Methylation# Methylation Calls