Resource
| Id | Histone_ChIP-seq/ENCSR546SDM |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR546SDM [biosample_summary="Homo sapiens CD4-positive, alpha-beta T cell" and target="H3K27ac"] |
| Description |
status: released biological_replicates: Rep 2 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN097LNN|/analyses/ENCAN097LNN/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_warning: Processed redacted alignments file {ENCFF058CQG|/files/ENCFF058CQG/} processed by ChIP-seq ENCODE4 v1.7.0 GRCh38 pipeline has 16419250 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 redacted alignments file {ENCFF058CQG|/files/ENCFF058CQG/} processed by ChIP-seq ENCODE4 v1.7.0 GRCh38 pipeline was generated from a library with PBC1 value of 0.88. 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 redacted alignments file {ENCFF058CQG|/files/ENCFF058CQG/} processed by ChIP-seq ENCODE4 v1.7.0 GRCh38 pipeline was generated from a library with PBC2 value of 8.51. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR546SDM | float |
Histone_ChIP-seq_ENCSR546SDM |
Histone_ChIP-seq ENCSR546SDM [biosample_summary="Homo sapiens CD4-positive, alpha-beta T cell" and target="H3K27ac"]
|
 |
[2.34, 85.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 36831060 | 1.14% | 29598 |
| chr1 | 3853300 | 1.55% | 3021 |
| chr2 | 2757505 | 1.14% | 2187 |
| chr3 | 2075437 | 1.05% | 1723 |
| chr4 | 1146930 | 0.60% | 934 |
| chr5 | 1823384 | 1.00% | 1356 |
| chr6 | 2078828 | 1.22% | 1650 |
| chr7 | 1571516 | 0.99% | 1336 |
| chr8 | 1139598 | 0.79% | 996 |
| chr9 | 1397930 | 1.01% | 1076 |
| chr10 | 1571823 | 1.17% | 1256 |
| chr11 | 2096273 | 1.55% | 1516 |
| chr12 | 1974468 | 1.48% | 1567 |
| chr13 | 770678 | 0.67% | 594 |
| chr14 | 1576683 | 1.47% | 1125 |
| chr15 | 1134175 | 1.11% | 902 |
| chr16 | 1461693 | 1.62% | 1275 |
| chr17 | 2266962 | 2.72% | 1796 |
| chr18 | 482682 | 0.60% | 409 |
| chr19 | 2165688 | 3.69% | 1850 |
| chr20 | 992526 | 1.54% | 838 |
| chr21 | 434863 | 0.93% | 363 |
| chr22 | 1020849 | 2.01% | 794 |
| chrX | 1021067 | 0.65% | 1007 |
| chrY | 16202 | 0.03% | 27 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 29598 | 245 | 54975 | 1244.38 | 843 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF941FZG.bed.gz | 713.18 KB | e946617092678ccff96d871299aed8c7 |
| ENCFF941FZG.tabix.bed.gz | 323.44 KB | 0750aca45cd4d16218980391eeb84a3e |
| ENCFF941FZG.tabix.bed.gz.tbi | 121.02 KB | 538e1d4e510339cba80beac63f122cd6 |
| genomic_resource.yaml | 3.36 KB | 2f6554526ca6a7114de149e0fd4ebee4 |
| statistics/ |