Resource
| Id | Histone_ChIP-seq/ENCSR054IRX |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR054IRX [biosample_summary="Homo sapiens IMR-90" and target="H2BK20ac"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN841NAA|/analyses/ENCAN841NAA/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_warning: Processed alignments file {ENCFF774KAG|/files/ENCFF774KAG/} processed by ChIP-seq ENCODE3 hg19 pipeline has 11036329 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H2BK20ac-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 {ENCFF135VSC|/files/ENCFF135VSC/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.82. 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 {ENCFF135VSC|/files/ENCFF135VSC/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 5.87. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR054IRX | float |
Histone_ChIP-seq_ENCSR054IRX |
Histone_ChIP-seq ENCSR054IRX [biosample_summary="Homo sapiens IMR-90" and target="H2BK20ac"]
|
 |
[1.76, 42.3] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 75508783 | 2.35% | 177711 |
| chr1 | 6529955 | 2.62% | 15256 |
| chr2 | 7447026 | 3.07% | 17061 |
| chr3 | 5140584 | 2.59% | 12133 |
| chr4 | 3744549 | 1.97% | 9657 |
| chr5 | 5032881 | 2.77% | 11661 |
| chr6 | 4647887 | 2.72% | 11784 |
| chr7 | 3602713 | 2.26% | 8887 |
| chr8 | 4066897 | 2.80% | 9701 |
| chr9 | 3419025 | 2.47% | 7807 |
| chr10 | 3650930 | 2.73% | 8491 |
| chr11 | 4354646 | 3.22% | 9841 |
| chr12 | 3697308 | 2.77% | 8937 |
| chr13 | 2157629 | 1.89% | 5373 |
| chr14 | 2360486 | 2.21% | 5425 |
| chr15 | 2912802 | 2.86% | 6420 |
| chr16 | 1956366 | 2.17% | 4195 |
| chr17 | 2834473 | 3.40% | 6231 |
| chr18 | 1919023 | 2.39% | 4635 |
| chr19 | 1015299 | 1.73% | 2600 |
| chr20 | 1800435 | 2.79% | 3922 |
| chr21 | 1170151 | 2.51% | 2717 |
| chr22 | 1110033 | 2.18% | 2437 |
| chrX | 937685 | 0.60% | 2540 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 177711 | 120 | 10336 | 424.9 | 313 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF237BCI.bed.gz | 4.03 MB | 9e669678c5531b2ef028b6dc87cb00bf |
| ENCFF237BCI.tabix.bed.gz | 1.78 MB | 9f74c3ecbfdeb7cca0abca78ad0cb991 |
| ENCFF237BCI.tabix.bed.gz.tbi | 289.53 KB | edb9a64e9b7f9f322d46f9f646330ad8 |
| genomic_resource.yaml | 3.17 KB | 97d4d5cfbbb6e5b603b299b9441905d4 |
| statistics/ |