Resource
| Id | Histone_ChIP-seq/ENCSR401CJA |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR401CJA [biosample_summary="Homo sapiens common myeloid progenitor, CD34-positive female adult (33 years)" and target="H3K4me1"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (33 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN322CVP|/analyses/ENCAN322CVP/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_not_compliant: Processed redacted alignments file {ENCFF987NMA|/files/ENCFF987NMA/} processed by ChIP-seq ENCODE4 v1.7.1 GRCh38 pipeline has 10087544 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me1-human and investigated as a broad histone mark is 20 million usable fragments. The recommended value is > 45 million, but > 35 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 {ENCFF987NMA|/files/ENCFF987NMA/} processed by ChIP-seq ENCODE4 v1.7.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.85. 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 {ENCFF987NMA|/files/ENCFF987NMA/} processed by ChIP-seq ENCODE4 v1.7.1 GRCh38 pipeline was generated from a library with PBC2 value of 6.59. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR401CJA | float |
Histone_ChIP-seq_ENCSR401CJA |
Histone_ChIP-seq ENCSR401CJA [biosample_summary="Homo sapiens common myeloid progenitor, CD34-positive female adult (33 years)" and target="H3K4me1"]
|
 |
[2.25, 31.2] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 91740417 | 2.85% | 120691 |
| chr1 | 9144226 | 3.67% | 11767 |
| chr2 | 6866278 | 2.84% | 9286 |
| chr3 | 5456946 | 2.75% | 7601 |
| chr4 | 3292374 | 1.73% | 4913 |
| chr5 | 4230274 | 2.33% | 5844 |
| chr6 | 5009440 | 2.93% | 7179 |
| chr7 | 4477117 | 2.81% | 6130 |
| chr8 | 3571387 | 2.46% | 4973 |
| chr9 | 4050159 | 2.93% | 5112 |
| chr10 | 4323474 | 3.23% | 5661 |
| chr11 | 5003362 | 3.70% | 6126 |
| chr12 | 4821570 | 3.62% | 6235 |
| chr13 | 1906661 | 1.67% | 2839 |
| chr14 | 3101180 | 2.90% | 3990 |
| chr15 | 3199791 | 3.14% | 4044 |
| chr16 | 3702865 | 4.10% | 4443 |
| chr17 | 5512558 | 6.62% | 6338 |
| chr18 | 1655202 | 2.06% | 2401 |
| chr19 | 4426071 | 7.55% | 5294 |
| chr20 | 2718094 | 4.22% | 3391 |
| chr21 | 1238981 | 2.65% | 1623 |
| chr22 | 2498031 | 4.92% | 2874 |
| chrX | 1534376 | 0.98% | 2627 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 120691 | 170 | 19902 | 760.13 | 553 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF705SRJ.bed.gz | 2.43 MB | d180367409d44cb8f6b85f174639707b |
| ENCFF705SRJ.tabix.bed.gz | 1.17 MB | 5b8ad5df6183d45d5f26cffa6b744db5 |
| ENCFF705SRJ.tabix.bed.gz.tbi | 318.26 KB | 3b126bbdd5676ab42cfc16fbe556b2de |
| genomic_resource.yaml | 3.36 KB | 9d945ef339a7acc0281d5ae375917e6f |
| statistics/ |