Resource
| Id | Histone_ChIP-seq/ENCSR254XTB |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR254XTB [biosample_summary="Homo sapiens neutrophil male" and target="H3K27me3"] |
| Description |
status: released biological_replicates: Rep 1 summary: male output_type: pseudoreplicated peaks audit_internal_action: Archived analysis {ENCAN750TKR|/analyses/ENCAN750TKR/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF073HXA|/files/ENCFF073HXA/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 8013838 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K27me3-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 alignments file {ENCFF073HXA|/files/ENCFF073HXA/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.90. 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 {ENCFF073HXA|/files/ENCFF073HXA/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 9.66. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR254XTB | float |
Histone_ChIP-seq_ENCSR254XTB |
Histone_ChIP-seq ENCSR254XTB [biosample_summary="Homo sapiens neutrophil male" and target="H3K27me3"]
|
 |
[2.21, 23.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 52491646 | 1.63% | 73933 |
| chr1 | 5456559 | 2.19% | 7700 |
| chr1_KI270713v1_random | 1784 | 4.38% | 3 |
| chr2 | 3885972 | 1.60% | 5461 |
| chr3 | 2335880 | 1.18% | 3274 |
| chr4 | 1955798 | 1.03% | 2457 |
| chr5 | 2975106 | 1.64% | 4016 |
| chr6 | 3230799 | 1.89% | 4341 |
| chr7 | 2394729 | 1.50% | 3175 |
| chr8 | 2286024 | 1.58% | 3191 |
| chr9 | 2279191 | 1.65% | 3344 |
| chr10 | 2833490 | 2.12% | 4036 |
| chr11 | 2940017 | 2.18% | 4326 |
| chr12 | 2554116 | 1.92% | 3402 |
| chr13 | 1312821 | 1.15% | 1845 |
| chr14 | 1809158 | 1.69% | 2545 |
| chr15 | 2060546 | 2.02% | 3050 |
| chr16 | 1655480 | 1.83% | 2367 |
| chr17 | 3133696 | 3.76% | 4304 |
| chr17_GL000205v2_random | 7449 | 4.01% | 6 |
| chr18 | 1067198 | 1.33% | 1586 |
| chr19 | 2174329 | 3.71% | 3062 |
| chr20 | 1998584 | 3.10% | 3069 |
| chr21 | 513922 | 1.10% | 803 |
| chr22 | 952302 | 1.87% | 1435 |
| chr22_KI270733v1_random | 1755 | 0.98% | 5 |
| chrUn_GL000219v1 | 1660 | 0.93% | 2 |
| chrX | 663220 | 0.43% | 1115 |
| chrY | 10061 | 0.02% | 13 |
| 3338 contigs with no values (128491779 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 73933 | 185 | 23512 | 709.99 | 443 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF073FHE.bed.gz | 1.33 MB | 3c2fcf5bad35e88d9fc3c621a6b41f95 |
| ENCFF073FHE.tabix.bed.gz | 700.04 KB | bf0c9f5af26750f90c20d762a1674d13 |
| ENCFF073FHE.tabix.bed.gz.tbi | 193.09 KB | 5632f05732f77b1481cae254826c4e98 |
| genomic_resource.yaml | 3.13 KB | aa12e0d085ef697fa630d2eb301eafce |
| statistics/ |