Bismark

Bismark Processing Report

bis_Pico22n_R1.fastq.gz

Data processed at 04:21:27 on 2022-01-11


Alignment Stats

Sequences analysed in total 84606
Single-end alignments with a unique best hit 43426
Sequences without alignments under any condition 38812
Sequences that did not map uniquely 2368
Genomic sequence context not extractable (edges of chromosomes) 0

Cytosine Methylation

Total C's analysed 988745
Methylated C's in CpG context 27977
Methylated C's in CHG context 46136
Methylated C's in CHH context 111272
Methylated C's in Unknown context 685
Unmethylated C's in CpG context 23469
Unmethylated C's in CHG context 201457
Unmethylated C's in CHH context 578434
Unmethylated C's in Unknown context 3211
Percentage methylation (CpG context) 54.4%
Percentage methylation (CHG context) 18.6%
Percentage methylation (CHH context) 16.1%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 9214 original top strand
CTOT 12575 complementary to original top strand
CTOB 12393 complementary to original bottom strand
OB 9244 original bottom strand

Deduplication

Alignments analysed 86844
Unique alignments 42082
Duplicates removed 44762
Duplicated alignments were found at 42072 different positions

Cytosine Methylation after Extraction

Total C's analysed 615438
Methylated C's in CpG context 17340
Methylated C's in CHG context 24805
Methylated C's in CHH context 59267
Unmethylated C's in CpG context 13871
Unmethylated C's in CHG context 128390
Unmethylated C's in CHH context 371765
Percentage methylation (CpG context) 55.6%
Percentage methylation (CHG context) 16.2%
Percentage methylation (CHH context) 13.8%

Nucleotide Coverage

Nucleotide Class Counts Sample Counts Genome% in Sample % in Genome fold coverage
A 679063 294005666 29.36 29.12 0.002
T 668788 294285704 28.92 29.15 0.002
C 461299 210594019 19.95 20.86 0.002
G 503613 210590343 21.78 20.86 0.002
AC 116760 52532529 5.10 5.20 0.002
CA 172048 77472169 7.51 7.67 0.002
TC 132773 60093701 5.79 5.95 0.002
CT 160358 73354317 7.00 7.27 0.002
CC 101149 48375161 4.41 4.79 0.002
CG 23406 11392056 1.02 1.13 0.002
GC 106355 49592331 4.64 4.91 0.002
GG 116336 48349387 5.08 4.79 0.002
AG 175354 73308184 7.65 7.26 0.002
GA 148999 60059654 6.50 5.95 0.002
TG 183832 77540413 8.02 7.68 0.002
GT 127180 52588666 5.55 5.21 0.002
TT 210115 96125962 9.17 9.52 0.002
TA 135608 60525298 5.92 6.00 0.002
AT 164805 72216445 7.19 7.15 0.002
AA 216271 95948192 9.44 9.50 0.002

M-Bias Plot