Bismark

Bismark Processing Report

/gscratch/srlab/sr320/data/cg-big/zr3644_9_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_9_R2.fq.gz

Data processed at 23:10:11 on 2021-06-09


Alignment Stats

Sequence pairs analysed in total 100000
Paired-end alignments with a unique best hit 61092
Pairs without alignments under any condition 20677
Pairs that did not map uniquely 18231
Genomic sequence context not extractable (edges of chromosomes) 0

Cytosine Methylation

Total C's analysed 2114911
Methylated C's in CpG context 29822
Methylated C's in CHG context 1724
Methylated C's in CHH context 7855
Methylated C's in Unknown context 76
Unmethylated C's in CpG context 245639
Unmethylated C's in CHG context 368266
Unmethylated C's in CHH context 1461605
Unmethylated C's in Unknown context 5097
Percentage methylation (CpG context) 10.8%
Percentage methylation (CHG context) 0.5%
Percentage methylation (CHH context) 0.5%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 15406 original top strand
CTOT 14990 complementary to original top strand
CTOB 15383 complementary to original bottom strand
OB 15313 original bottom strand

Deduplication

Alignments analysed 61092
Unique alignments 56719
Duplicates removed 4373
Duplicated alignments were found at 4076 different positions

Cytosine Methylation after Extraction

Total C's analysed 1283697
Methylated C's in CpG context 17534
Methylated C's in CHG context 1072
Methylated C's in CHH context 4784
Unmethylated C's in CpG context 147837
Unmethylated C's in CHG context 221612
Unmethylated C's in CHH context 890858
Percentage methylation (CpG context) 10.6%
Percentage methylation (CHG context) 0.5%
Percentage methylation (CHH context) 0.5%

M-Bias Plot