Bismark

Bismark Processing Report

/Volumes/web/seashell/bu-serine-wd/18-04-07/zr2096_1_s1_R1.fastq.gz and /Volumes/web/seashell/bu-serine-wd/18-04-07/zr2096_1_s1_R2.fastq.gz

Data processed at 17:48 on 2018-09-21

Alignment Stats

Sequence pairs analysed in total 100000
Paired-end alignments with a unique best hit 13744
Pairs without alignments under any condition 81302
Pairs that did not map uniquely 4954
Genomic sequence context not extractable (edges of chromosomes) 0

Cytosine Methylation

Total C's analysed 481569
Methylated C's in CpG context 47945
Methylated C's in CHG context 2774
Methylated C's in CHH context 7846
Methylated C's in Unknown context 624
Unmethylated C's in CpG context 17126
Unmethylated C's in CHG context 107925
Unmethylated C's in CHH context 297953
Unmethylated C's in Unknown context 1993
Percentage methylation (CpG context) 73.7%
Percentage methylation (CHG context) 2.5%
Percentage methylation (CHH context) 2.6%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 3402 original top strand
CTOT 3480 complementary to original top strand
CTOB 3458 complementary to original bottom strand
OB 3404 original bottom strand

Cytosine Methylation after Extraction

Total C's analysed 304266
Methylated C's in CpG context 29931
Methylated C's in CHG context 1873
Methylated C's in CHH context 5172
Unmethylated C's in CpG context 10904
Unmethylated C's in CHG context 67806
Unmethylated C's in CHH context 188580
Percentage methylation (CpG context) 73.3%
Percentage methylation (CHG context) 2.7%
Percentage methylation (CHH context) 2.7%

Nucleotide Coverage

Nucleotide Class Counts Sample Counts Genome% in Sample % in Genome fold coverage
A 397765 223134775 27.39 32.59 0.002
T 417399 223043757 28.74 32.58 0.002
C 290760 119229119 20.02 17.41 0.002
G 346559 119267677 23.86 17.42 0.003
AC 77775 37359527 5.42 5.46 0.002
CA 96576 45827414 6.73 6.69 0.002
TC 85855 38778132 5.98 5.66 0.002
CT 84353 35498217 5.87 5.18 0.002
CC 66568 23444678 4.64 3.42 0.003
CG 39753 14458703 2.77 2.11 0.003
GC 57424 19646670 4.00 2.87 0.003
GG 86627 23423030 6.03 3.42 0.004
AG 95546 35548672 6.65 5.19 0.003
GA 100972 38810489 7.03 5.67 0.003
TG 119602 45837169 8.33 6.69 0.003
GT 95958 37387368 6.68 5.46 0.003
TT 126771 80726644 8.83 11.79 0.002
TA 80967 57701608 5.64 8.43 0.001
AT 105707 69431301 7.36 10.14 0.002
AA 115616 80795037 8.05 11.80 0.001

M-Bias Plot