Resource
| Id | Histone_ChIP-seq/ENCSR210ZPC |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR210ZPC [biosample_summary="Homo sapiens smooth muscle cell originated from H9" and target="H3K27ac"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: female embryo (5 days) output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN331MWF|/analyses/ENCAN331MWF/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_warning: Processed alignments file {ENCFF699GFE|/files/ENCFF699GFE/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 11682473 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K27ac-human and investigated as a narrow histone mark is 10 million usable fragments. The recommended value is > 20 million, but > 10 million is acceptable. (See {ENCODE ChIP-seq data standards|/data-standards/chip-seq/}) audit_warning: PBC1 (PCR Bottlenecking Coefficient 1, M1/M_distinct) is the ratio of the number of genomic locations where exactly one read maps uniquely (M1) to the number of genomic locations where some reads map (M_distinct). A PBC1 value in the range 0 - 0.5 is severe bottlenecking, 0.5 - 0.8 is moderate bottlenecking, 0.8 - 0.9 is mild bottlenecking, and > 0.9 is no bottlenecking. PBC1 value > 0.9 is recommended, but > 0.8 is acceptable. ENCODE processed alignments file {ENCFF821PAH|/files/ENCFF821PAH/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.89. audit_warning: PBC2 (PCR Bottlenecking Coefficient 2, M1/M2) is the ratio of the number of genomic locations where exactly one read maps uniquely (M1) to the number of genomic locations where two reads map uniquely (M2). A PBC2 value in the range 0 - 1 is severe bottlenecking, 1 - 3 is moderate bottlenecking, 3 - 10 is mild bottlenecking, > 10 is no bottlenecking. PBC2 value > 10 is recommended, but > 3 is acceptable. ENCODE processed alignments file {ENCFF821PAH|/files/ENCFF821PAH/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 9.56. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR210ZPC | float |
Histone_ChIP-seq_ENCSR210ZPC |
Histone_ChIP-seq ENCSR210ZPC [biosample_summary="Homo sapiens smooth muscle cell originated from H9" and target="H3K27ac"]
|
 |
[1.3, 51.1] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 154441782 | 4.80% | 103634 |
| chr1 | 13928072 | 5.59% | 9242 |
| chr1_KI270713v1_random | 1323 | 3.25% | 3 |
| chr2 | 13068288 | 5.40% | 8591 |
| chr3 | 10778357 | 5.44% | 7063 |
| chr4 | 8202646 | 4.31% | 5492 |
| chr5 | 9804322 | 5.40% | 6443 |
| chr6 | 9621220 | 5.63% | 6568 |
| chr7 | 7651490 | 4.80% | 5304 |
| chr8 | 7362943 | 5.07% | 5109 |
| chr9 | 6705712 | 4.85% | 4434 |
| chr10 | 7519367 | 5.62% | 5010 |
| chr11 | 8218537 | 6.08% | 5317 |
| chr12 | 8093423 | 6.07% | 5201 |
| chr13 | 4377153 | 3.83% | 3039 |
| chr14 | 5421592 | 5.06% | 3460 |
| chr15 | 5119496 | 5.02% | 3411 |
| chr16 | 4024515 | 4.45% | 2889 |
| chr17 | 5977779 | 7.18% | 4013 |
| chr17_GL000205v2_random | 2607 | 1.40% | 3 |
| chr18 | 3808036 | 4.74% | 2514 |
| chr19 | 3309576 | 5.65% | 2375 |
| chr20 | 3431867 | 5.33% | 2417 |
| chr21 | 2149052 | 4.60% | 1361 |
| chr22 | 2378704 | 4.68% | 1583 |
| chr22_KI270733v1_random | 406 | 0.23% | 1 |
| chrUn_GL000195v1 | 2589 | 1.42% | 1 |
| chrUn_KI270467v1 | 660 | 16.84% | 1 |
| chrX | 3482050 | 2.23% | 2789 |
| 3338 contigs with no values (185711576 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 103634 | 230 | 55468 | 1490.26 | 1001 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF002NFJ.bed.gz | 2.68 MB | 030e98301139042799675fefd1cfdacc |
| ENCFF002NFJ.tabix.bed.gz | 1.13 MB | 6dcf90ac0e264271a5cf3008d412fd13 |
| ENCFF002NFJ.tabix.bed.gz.tbi | 332.14 KB | 94dad343fc6703561068246a822a232e |
| genomic_resource.yaml | 3.24 KB | ad8fde658cc1df009a5deb73b9d5e8d0 |
| statistics/ |