Resource
| Id | Histone_ChIP-seq/ENCSR797GOJ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR797GOJ [biosample_summary="Homo sapiens CD8-positive, alpha-beta T cell" and target="H3K27me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN993VOW|/analyses/ENCAN993VOW/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed redacted alignments file {ENCFF504BFM|/files/ENCFF504BFM/} processed by ChIP-seq ENCODE3 hg19 pipeline has 13041431 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_not_compliant: Processed redacted alignments file {ENCFF955QEC|/files/ENCFF955QEC/} processed by ChIP-seq ENCODE3 hg19 pipeline has 14663363 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 redacted alignments file {ENCFF955QEC|/files/ENCFF955QEC/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.86. 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 {ENCFF955QEC|/files/ENCFF955QEC/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 6.93. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR797GOJ | float |
Histone_ChIP-seq_ENCSR797GOJ |
Histone_ChIP-seq ENCSR797GOJ [biosample_summary="Homo sapiens CD8-positive, alpha-beta T cell" and target="H3K27me3"]
|
 |
[1.5, 11.8] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 10893940 | 0.34% | 18732 |
| chr1 | 1050801 | 0.42% | 1877 |
| chr2 | 910220 | 0.38% | 1482 |
| chr3 | 470131 | 0.24% | 883 |
| chr4 | 474485 | 0.25% | 848 |
| chr5 | 683960 | 0.38% | 1159 |
| chr6 | 813557 | 0.48% | 1356 |
| chr7 | 568770 | 0.36% | 914 |
| chr8 | 462716 | 0.32% | 824 |
| chr9 | 477311 | 0.34% | 847 |
| chr10 | 635441 | 0.47% | 1081 |
| chr11 | 541803 | 0.40% | 955 |
| chr12 | 524177 | 0.39% | 873 |
| chr13 | 278919 | 0.24% | 473 |
| chr14 | 333114 | 0.31% | 614 |
| chr15 | 447885 | 0.44% | 778 |
| chr16 | 275291 | 0.30% | 504 |
| chr17 | 605371 | 0.73% | 871 |
| chr18 | 180912 | 0.23% | 369 |
| chr19 | 544755 | 0.93% | 867 |
| chr20 | 307827 | 0.48% | 585 |
| chr21 | 79268 | 0.17% | 157 |
| chr22 | 182215 | 0.36% | 330 |
| chrX | 45011 | 0.03% | 85 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 18732 | 215 | 8640 | 581.57 | 452 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF775AXL.bed.gz | 359.93 KB | 7200df4fef0717df6e83f4e934df6398 |
| ENCFF775AXL.tabix.bed.gz | 185.57 KB | fa47b95bcc5dc994e76b663a03ad32d1 |
| ENCFF775AXL.tabix.bed.gz.tbi | 92.66 KB | 6aa244536d107a9bfe0cb511261eac2d |
| genomic_resource.yaml | 3.85 KB | 53f22dc9c8c86cf63b6a018b7884fed3 |
| statistics/ |