Resource
| Id | Histone_ChIP-seq/ENCSR564IGJ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR564IGJ [biosample_summary="Homo sapiens SK-N-SH" and target="H3K27ac"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN102RKI|/analyses/ENCAN102RKI/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_internal_action: Released analysis {ENCAN102RKI|/analyses/ENCAN102RKI/} has in progress subobject document {17179091-b535-41d2-9139-d14de56ca785|/documents/17179091-b535-41d2-9139-d14de56ca785/} audit_warning: Processed alignments file {ENCFF098JJI|/files/ENCFF098JJI/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 15311922 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 {ENCFF098JJI|/files/ENCFF098JJI/} 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 {ENCFF098JJI|/files/ENCFF098JJI/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 5.79. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR564IGJ | float |
Histone_ChIP-seq_ENCSR564IGJ |
Histone_ChIP-seq ENCSR564IGJ [biosample_summary="Homo sapiens SK-N-SH" and target="H3K27ac"]
|
 |
[1.58, 135] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 112945072 | 3.51% | 69317 |
| chr1 | 10915023 | 4.38% | 6634 |
| chr2 | 9618335 | 3.97% | 5901 |
| chr3 | 8016725 | 4.04% | 4903 |
| chr4 | 6003990 | 3.16% | 3740 |
| chr5 | 7106656 | 3.91% | 4123 |
| chr6 | 6943210 | 4.06% | 4164 |
| chr7 | 5904380 | 3.71% | 3575 |
| chr8 | 5012352 | 3.45% | 3123 |
| chr9 | 4653106 | 3.36% | 2916 |
| chr10 | 5687307 | 4.25% | 3416 |
| chr11 | 5901228 | 4.37% | 3376 |
| chr12 | 6162981 | 4.62% | 3584 |
| chr13 | 3114943 | 2.72% | 1993 |
| chr14 | 3407875 | 3.18% | 2077 |
| chr15 | 4047560 | 3.97% | 2375 |
| chr16 | 2972592 | 3.29% | 2026 |
| chr17 | 4773826 | 5.73% | 2931 |
| chr18 | 2166709 | 2.70% | 1419 |
| chr19 | 2673149 | 4.56% | 1869 |
| chr20 | 2533021 | 3.93% | 1639 |
| chr21 | 1126979 | 2.41% | 744 |
| chr22 | 1608792 | 3.17% | 1020 |
| chrX | 2594333 | 1.66% | 1769 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 69317 | 233 | 64293 | 1629.4 | 1200 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF138VUT.bed.gz | 1.93 MB | be94e1a5a7204241b0fabf05966a6147 |
| ENCFF138VUT.tabix.bed.gz | 804.39 KB | 913694a443485aff11c66935160b9109 |
| ENCFF138VUT.tabix.bed.gz.tbi | 257.97 KB | f4df6143361c8de91937803e17c9e87e |
| genomic_resource.yaml | 3.41 KB | 45d0b69242a079f76285fcdf0e271911 |
| statistics/ |