Alignment Stats
| Sequence pairs analysed in total |
39972937 |
| Paired-end alignments with a unique best hit |
23177857 |
| Pairs without alignments under any condition |
4129941 |
| Pairs that did not map uniquely |
12665139 |
| Genomic sequence context not extractable (edges of chromosomes) |
1 |
|
|
Cytosine Methylation
| Total C's analysed |
1021026796 |
| Methylated C's in CpG context |
25994008 |
| Methylated C's in CHG context |
1280085 |
| Methylated C's in CHH context |
5688786 |
| Methylated C's in Unknown context |
128202 |
| Unmethylated C's in CpG context |
100204693 |
| Unmethylated C's in CHG context |
173177972 |
| Unmethylated C's in CHH context |
714681252 |
| Unmethylated C's in Unknown context |
907886 |
| Percentage methylation (CpG context) |
20.6% |
| Percentage methylation (CHG context) |
0.7% |
| Percentage methylation (CHH context) |
0.8% |
| Methylated C's in Unknown context |
12.4% |
|
|
Alignment to Individual Bisulfite Strands
| OT |
11598063 |
original top strand |
| CTOT |
0 |
complementary to original top strand |
| CTOB |
0 |
complementary to original bottom strand |
| OB |
11579793 |
original bottom strand |
|
|
Deduplication
| Alignments analysed |
23177856 |
| Unique alignments |
22017337 |
| Duplicates removed |
1160519 |
| Duplicated alignments were found at 1107100 different positions |
|
|
Cytosine Methylation after Extraction
| Total C's analysed |
743967875 |
| Methylated C's in CpG context |
18882208 |
| Methylated C's in CHG context |
826268 |
| Methylated C's in CHH context |
3697250 |
| Unmethylated C's in CpG context |
73142403 |
| Unmethylated C's in CHG context |
126206915 |
| Unmethylated C's in CHH context |
521212831 |
| Percentage methylation (CpG context) |
20.5% |
| Percentage methylation (CHG context) |
N/A% |
| Percentage methylation (CHH context) |
N/A% |
|
|
Nucleotide Coverage
| Nucleotide Class | Counts Sample | Counts Genome | % in Sample | % in Genome | fold coverage |
|---|
| A | 1894884749 | 378413849 | 34.56 | 32.06 | 5.007 |
|---|
| T | 1746351566 | 378309330 | 31.85 | 32.05 | 4.616 |
|---|
| C | 870237807 | 211781786 | 15.87 | 17.94 | 4.109 |
|---|
| G | 970874593 | 211810957 | 17.71 | 17.95 | 4.584 |
|---|
| AC | 297607021 | 68264877 | 5.47 | 5.78 | 4.360 |
|---|
| CA | 358695361 | 80836853 | 6.59 | 6.85 | 4.437 |
|---|
| TC | 274310503 | 67705770 | 5.04 | 5.74 | 4.052 |
|---|
| CT | 247326285 | 62481783 | 4.54 | 5.29 | 3.958 |
|---|
| CC | 150583552 | 42358709 | 2.77 | 3.59 | 3.555 |
|---|
| CG | 106898193 | 26104181 | 1.96 | 2.21 | 4.095 |
|---|
| GC | 141428676 | 33452245 | 2.60 | 2.83 | 4.228 |
|---|
| GG | 177487989 | 42378301 | 3.26 | 3.59 | 4.188 |
|---|
| AG | 302771058 | 62424886 | 5.56 | 5.29 | 4.850 |
|---|
| GA | 333377059 | 67679435 | 6.12 | 5.73 | 4.926 |
|---|
| TG | 376743857 | 80903356 | 6.92 | 6.85 | 4.657 |
|---|
| GT | 311461332 | 68300800 | 5.72 | 5.79 | 4.560 |
|---|
| TT | 590107171 | 128294772 | 10.84 | 10.87 | 4.600 |
|---|
| TA | 492767413 | 101400983 | 9.05 | 8.59 | 4.860 |
|---|
| AT | 585281802 | 119230832 | 10.75 | 10.10 | 4.909 |
|---|
| AA | 696224118 | 128492079 | 12.79 | 10.89 | 5.418 |
|---|
|
|
M-Bias Plot
