Resource
| Id | Histone_ChIP-seq/ENCSR152QRE |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR152QRE [biosample_summary="Homo sapiens SK-N-MC" and target="H3K4me1"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN327QTY|/analyses/ENCAN327QTY/} has in progress subobject document {eb22d2f5-f697-4d59-b32c-7142c8606191|/documents/eb22d2f5-f697-4d59-b32c-7142c8606191/} audit_internal_action: Released analysis {ENCAN327QTY|/analyses/ENCAN327QTY/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_warning: Processed alignments file {ENCFF493XFX|/files/ENCFF493XFX/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 36861664 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me1-human and investigated as a broad histone mark is 20 million usable fragments. The recommended value is > 45 million, but > 35 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 {ENCFF493XFX|/files/ENCFF493XFX/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.83. 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 {ENCFF493XFX|/files/ENCFF493XFX/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 5.77. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR152QRE | float |
Histone_ChIP-seq_ENCSR152QRE |
Histone_ChIP-seq ENCSR152QRE [biosample_summary="Homo sapiens SK-N-MC" and target="H3K4me1"]
|
 |
[1.53, 13.2] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 134335148 | 4.18% | 152354 |
| chr1 | 11973123 | 4.81% | 13308 |
| chr2 | 13254733 | 5.47% | 14597 |
| chr3 | 9092391 | 4.59% | 10185 |
| chr4 | 8520619 | 4.48% | 10159 |
| chr5 | 8074972 | 4.45% | 9125 |
| chr6 | 10973256 | 6.42% | 12081 |
| chr7 | 7691120 | 4.83% | 8736 |
| chr8 | 10807267 | 7.45% | 10172 |
| chr9 | 5753949 | 4.16% | 6285 |
| chr10 | 2562140 | 1.91% | 4260 |
| chr11 | 5833763 | 4.32% | 6500 |
| chr12 | 7297070 | 5.48% | 8391 |
| chr13 | 5098299 | 4.46% | 5654 |
| chr14 | 5139478 | 4.80% | 5552 |
| chr15 | 3723450 | 3.65% | 4179 |
| chr16 | 1778304 | 1.97% | 2540 |
| chr17 | 4048007 | 4.86% | 4724 |
| chr18 | 2581658 | 3.21% | 3303 |
| chr19 | 1889871 | 3.22% | 2490 |
| chr20 | 3281120 | 5.09% | 3529 |
| chr21 | 1569596 | 3.36% | 1817 |
| chr22 | 1828720 | 3.60% | 2131 |
| chrX | 1562242 | 1.00% | 2636 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 152354 | 215 | 20549 | 881.73 | 638 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF861QCD.bed.gz | 3.34 MB | 9587ac5caeccd77d25952cc039e1b71e |
| ENCFF861QCD.tabix.bed.gz | 1.56 MB | 6e3d7b32ed2bf265ce3e6549e97b44e6 |
| ENCFF861QCD.tabix.bed.gz.tbi | 393.2 KB | 1146b87efc8e820113773e9494135b06 |
| genomic_resource.yaml | 3.41 KB | 544083f7c6c0a9357bc576d455987403 |
| statistics/ |