Bismark

Bismark Processing Report

zr2096_8_s1_R1_val_1.fq.gz and zr2096_8_s1_R2_val_2.fq.gz

Data processed at 13:52 on 2018-04-27

Alignment

Sequence pairs analysed in total 1,000,000
Paired-end alignments with a unique best hit 481,891
Pairs without alignments under any condition 337,604
Pairs that did not map uniquely 180,505
Genomic sequence context not extractable (edges of chromosomes) 0
Created with Highcharts 5.0.5: 48.2 %Unique AlignmentsUnique Alignments: 48.2 %: 33.8 %No AlignmentNo Alignment: 33.8 %: 18.1 %Multiple AlignmentsMultiple Alignments: 18.1 %: 0.0 %No Genomic SequenceNo Genomic Sequence: 0.0 %

Cytosine Methylation

Total C's analysed 12,325,890
Methylated C's in CpG context 992,024
Methylated C's in CHG context 72,967
Methylated C's in CHH context 451,622
Methylated C's in Unknown context 42,077
Unmethylated C's in CpG context 486,713
Unmethylated C's in CHG context 2,574,344
Unmethylated C's in CHH context 7,748,220
Unmethylated C's in Unknown context 161,022
Percentage methylation (CpG context) 67.1%
Percentage methylation (CHG context) 2.8%
Percentage methylation (CHH context) 5.5%
Methylated C's in Unknown context N/A%
Created with Highcharts 5.0.5% MethylationCpGCHGCHH020406080100

Alignment to Individual Bisulfite Strands

OT 122,028 original top strand
CTOT 119,189 complementary to original top strand
CTOB 118,638 complementary to original bottom strand
OB 122,036 original bottom strand
Created with Highcharts 5.0.5Number of AlignmentsAlignment ContextOTCTOTCTOBOB025k50k75k100k125k150k

Deduplication

Alignments analysed 481,891
Unique alignments 479,306
Duplicates removed 2,585
Duplicated alignments were found at 1880 different positions
Created with Highcharts 5.0.5: 99.5 %UniqueUnique: 99.5 %: 0.5 %DuplicateDuplicate: 0.5 %

Cytosine Methylation after Extraction

Total C's analysed 8,111,311
Methylated C's in CpG context 644,017
Methylated C's in CHG context 48,503
Methylated C's in CHH context 271,288
Unmethylated C's in CpG context 323,510
Unmethylated C's in CHG context 1,689,076
Unmethylated C's in CHH context 5,134,917
Percentage methylation (CpG context) 66.6%
Percentage methylation (CHG context) 2.8%
Percentage methylation (CHH context) 5.0%
Created with Highcharts 5.0.5% MethylationCpGCHGCHH020406080100

M-Bias Plot

Created with Highcharts 5.0.5Position (bp)% Methylation# Methylation CallsRead 1Click and drag in the plot area to zoom inCpG MethylationCHG MethylationCHH MethylationCpG Total CallsCHG Total CallsCHH Total Calls051015202530354045505560657075800102030405060708090100010k20k30k40k50k60k70k
Created with Highcharts 5.0.5Position (bp)% Methylation# Methylation CallsRead 2Click and drag in the plot area to zoom inCpG MethylationCHG MethylationCHH MethylationCpG Total CallsCHG Total CallsCHH Total Calls05101520253035404550556065707580010203040506070809010005k10k15k20k25k30k35k40k45k50k