Resource
| Id | Histone_ChIP-seq/ENCSR554TZE |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR554TZE [biosample_summary="Homo sapiens H9" and target="H4K5ac"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN678JYO|/analyses/ENCAN678JYO/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_warning: Processed alignments file {ENCFF867GZF|/files/ENCFF867GZF/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 14255173 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 {ENCFF867GZF|/files/ENCFF867GZF/} processed by ChIP-seq ENCODE3 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 {ENCFF867GZF|/files/ENCFF867GZF/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 9.64. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR554TZE | float |
Histone_ChIP-seq_ENCSR554TZE |
Histone_ChIP-seq ENCSR554TZE [biosample_summary="Homo sapiens H9" and target="H4K5ac"]
|
 |
[1.66, 23] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 4746177 | 0.15% | 30209 |
| chr1 | 427561 | 0.17% | 2651 |
| chr2 | 387959 | 0.16% | 2498 |
| chr3 | 318166 | 0.16% | 2052 |
| chr4 | 266770 | 0.14% | 1759 |
| chr5 | 290606 | 0.16% | 1883 |
| chr6 | 292610 | 0.17% | 1860 |
| chr7 | 270763 | 0.17% | 1748 |
| chr8 | 225781 | 0.16% | 1484 |
| chr9 | 168021 | 0.12% | 1101 |
| chr10 | 208393 | 0.16% | 1346 |
| chr11 | 217094 | 0.16% | 1369 |
| chr12 | 248794 | 0.19% | 1562 |
| chr13 | 139160 | 0.12% | 919 |
| chr14 | 152465 | 0.14% | 957 |
| chr15 | 130261 | 0.13% | 843 |
| chr16 | 150386 | 0.17% | 955 |
| chr17 | 162381 | 0.20% | 995 |
| chr18 | 115531 | 0.14% | 754 |
| chr19 | 152863 | 0.26% | 897 |
| chr20 | 123865 | 0.19% | 756 |
| chr21 | 56571 | 0.12% | 363 |
| chr22 | 79772 | 0.16% | 466 |
| chr22_KI270733v1_random | 329 | 0.18% | 2 |
| chr22_KI270736v1_random | 105 | 0.06% | 1 |
| chrUn_KI270442v1 | 105 | 0.03% | 1 |
| chrX | 159865 | 0.10% | 987 |
| 3340 contigs with no values (185550747 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 30209 | 105 | 1058 | 157.11 | 138 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF993ETS.bed.gz | 572.75 KB | 1ade62499dbdd80926086b3261a2296b |
| ENCFF993ETS.tabix.bed.gz | 294.29 KB | 30c0c87802776ffecbbe001cdb57234b |
| ENCFF993ETS.tabix.bed.gz.tbi | 212.87 KB | 91e9d0ff7c81a2c0945d7020aa71a5b0 |
| genomic_resource.yaml | 3.15 KB | b0cbc2eb1297c6c9b2ee2a1a0e384b3a |
| statistics/ |