Resource
| Id | Histone_ChIP-seq/ENCSR706RRA |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR706RRA [biosample_summary="Homo sapiens IMR-90" and target="H4K5ac"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN152RKW|/analyses/ENCAN152RKW/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_internal_action: Released analysis {ENCAN152RKW|/analyses/ENCAN152RKW/} has in progress subobject document {91f05238-0c2e-4922-85a7-ce905d28e11f|/documents/91f05238-0c2e-4922-85a7-ce905d28e11f/} audit_warning: Processed alignments file {ENCFF095MHL|/files/ENCFF095MHL/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 12219693 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H4K5ac-human and investigated as a transcription factor 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 {ENCFF113XYR|/files/ENCFF113XYR/} processed by ChIP-seq ENCODE4 v1.6.1 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 {ENCFF113XYR|/files/ENCFF113XYR/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 9.65. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR706RRA | float |
Histone_ChIP-seq_ENCSR706RRA |
Histone_ChIP-seq ENCSR706RRA [biosample_summary="Homo sapiens IMR-90" and target="H4K5ac"]
|
 |
[1.56, 21.8] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 47838095 | 1.49% | 139690 |
| chr1 | 4180937 | 1.68% | 12168 |
| chr2 | 4577553 | 1.89% | 13171 |
| chr3 | 3247215 | 1.64% | 9600 |
| chr4 | 2198044 | 1.16% | 7022 |
| chr5 | 2888661 | 1.59% | 8459 |
| chr6 | 2877955 | 1.68% | 8758 |
| chr7 | 2292744 | 1.44% | 6932 |
| chr8 | 2284321 | 1.57% | 7009 |
| chr9 | 2202009 | 1.59% | 6286 |
| chr10 | 2051623 | 1.53% | 6081 |
| chr11 | 2851710 | 2.11% | 7931 |
| chr12 | 2396585 | 1.80% | 7134 |
| chr13 | 1251876 | 1.09% | 3926 |
| chr14 | 1543583 | 1.44% | 4413 |
| chr15 | 1922753 | 1.89% | 5249 |
| chr16 | 1453642 | 1.61% | 3807 |
| chr17 | 2065291 | 2.48% | 5539 |
| chr18 | 1016129 | 1.26% | 3138 |
| chr19 | 1248698 | 2.13% | 3517 |
| chr20 | 1125007 | 1.75% | 3106 |
| chr21 | 661593 | 1.42% | 2016 |
| chr22 | 829308 | 1.63% | 2190 |
| chrX | 670858 | 0.43% | 2238 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 139690 | 125 | 6135 | 342.46 | 263 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF742PFJ.bed.gz | 3.27 MB | f8dcc13b8d37cfdd3f16c8d8ad5b513c |
| ENCFF742PFJ.tabix.bed.gz | 1.42 MB | d33cd056ef3068a270c840e968d580d5 |
| ENCFF742PFJ.tabix.bed.gz.tbi | 287.06 KB | d75d341c5cb5e08b6d91cf59368e559c |
| genomic_resource.yaml | 3.41 KB | 69b99322c4e2702bc99118970373a4ea |
| statistics/ |