Bismark

Bismark Processing Report

/gscratch/srlab/sr320/data/olurida-bs/decomp//zr1394_3_s456_trimmed.fq

Data processed at 03:30 on 2022-07-03


Alignment Stats

Sequences analysed in total 48376729
Single-end alignments with a unique best hit 14759690
Sequences without alignments under any condition 14949228
Sequences that did not map uniquely 18667811
Genomic sequence context not extractable (edges of chromosomes) 0
30.5%30.9%38.6%0%
Unique AlignmentsNo AlignmentMultiple AlignmentsNo Genomic Sequence

Cytosine Methylation

Total C's analysed 89218342
Methylated C's in CpG context 11414576
Methylated C's in CHG context 405883
Methylated C's in CHH context 5151062
Methylated C's in Unknown context 3929
Unmethylated C's in CpG context 2383288
Unmethylated C's in CHG context 17125947
Unmethylated C's in CHH context 52737586
Unmethylated C's in Unknown context 27879
Percentage methylation (CpG context) 82.7%
Percentage methylation (CHG context) 2.3%
Percentage methylation (CHH context) 8.9%
Methylated C's in Unknown context N/A%
CpG contextCHG contextCHH context020406080100
% Methylation

Alignment to Individual Bisulfite Strands

OT 3305606 original top strand
CTOT 4103783 complementary to original top strand
CTOB 4068630 complementary to original bottom strand
OB 3281671 original bottom strand
OTCTOTCTOBOB00.5M1M1.5M2M2.5M3M3.5M4M
Number of Alignments

Deduplication

Alignments analysed 14759690
Unique alignments 10432199
Duplicates removed 4327491
Duplicated alignments were found at 1731966 different positions
70.7%29.3%
Unique AlignmentsDuplicate Alignments

Cytosine Methylation after Extraction

Total C's analysed 62129400
Methylated C's in CpG context 7053744
Methylated C's in CHG context 296595
Methylated C's in CHH context 4106276
Unmethylated C's in CpG context 1706032
Unmethylated C's in CHG context 11393779
Unmethylated C's in CHH context 37572974
Percentage methylation (CpG context) 80.5%
Percentage methylation (CHG context) 2.5%
Percentage methylation (CHH context) 9.9%
CpG contextCHH contextCHG context020406080100
% Methylation

M-Bias Plot

510152025300204060801000.2M0.4M0.6M0.8M1M1.2M1.4M
CpG methylationCHG methylationCHH methylationCpG total callsCHG total callsCHH total callsRead 1Position in Read [bp]% Methylation# Methylation Calls