Resource
| Id | Histone_ChIP-seq/ENCSR103GGR |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR103GGR [biosample_summary="Homo sapiens CD8-positive, alpha-beta T cell male adult (37 years)" and target="H3K27me3"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (37 years) output_type: pseudoreplicated peaks audit_internal_action: Archived analysis {ENCAN976SYL|/analyses/ENCAN976SYL/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF783NPA|/files/ENCFF783NPA/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 6884470 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 {ENCFF783NPA|/files/ENCFF783NPA/} processed by ChIP-seq ENCODE3 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 alignments file {ENCFF783NPA|/files/ENCFF783NPA/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 8.50. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR103GGR | float |
Histone_ChIP-seq_ENCSR103GGR |
Histone_ChIP-seq ENCSR103GGR [biosample_summary="Homo sapiens CD8-positive, alpha-beta T cell male adult (37 years)" and target="H3K27me3"]
|
 |
[2.11, 40.1] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 12891147 | 0.40% | 25401 |
| chr1 | 1180573 | 0.47% | 2392 |
| chr2 | 975596 | 0.40% | 1929 |
| chr3 | 503856 | 0.25% | 1119 |
| chr4 | 461464 | 0.24% | 990 |
| chr5 | 709971 | 0.39% | 1495 |
| chr6 | 843760 | 0.49% | 1696 |
| chr7 | 707277 | 0.44% | 1351 |
| chr8 | 500314 | 0.34% | 1027 |
| chr9 | 557893 | 0.40% | 1064 |
| chr10 | 646368 | 0.48% | 1327 |
| chr11 | 644554 | 0.48% | 1302 |
| chr12 | 609124 | 0.46% | 1228 |
| chr13 | 271522 | 0.24% | 554 |
| chr14 | 400287 | 0.37% | 848 |
| chr15 | 465433 | 0.46% | 931 |
| chr16 | 426553 | 0.47% | 799 |
| chr17 | 848034 | 1.02% | 1420 |
| chr17_GL000205v2_random | 3498 | 1.88% | 6 |
| chr18 | 176186 | 0.22% | 405 |
| chr19 | 987182 | 1.68% | 1585 |
| chr20 | 439435 | 0.68% | 860 |
| chr21 | 140729 | 0.30% | 298 |
| chr22 | 293589 | 0.58% | 574 |
| chr22_KI270733v1_random | 842 | 0.47% | 3 |
| chrUn_GL000195v1 | 340 | 0.19% | 1 |
| chrUn_GL000218v1 | 212 | 0.13% | 1 |
| chrUn_GL000219v1 | 270 | 0.15% | 1 |
| chrUn_GL000224v1 | 341 | 0.19% | 1 |
| chrUn_KI270438v1 | 607 | 0.54% | 2 |
| chrUn_KI270744v1 | 429 | 0.25% | 1 |
| chrUn_KI270754v1 | 295 | 0.73% | 1 |
| chrX | 91419 | 0.06% | 183 |
| chrY | 3194 | 0.01% | 7 |
| 3333 contigs with no values (127687620 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 25401 | 165 | 7700 | 507.51 | 391 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF565COF.bed.gz | 447.18 KB | 99c75c8fe8995c604fc4a5ac44ec4bd2 |
| ENCFF565COF.tabix.bed.gz | 236.46 KB | fc3ab971a45ad7e72eb0c3d936446b6f |
| ENCFF565COF.tabix.bed.gz.tbi | 122.23 KB | 7cdd4d016458948a9844a469b9fa539d |
| genomic_resource.yaml | 3.28 KB | 9de8d166592613b116bf15120dc45f56 |
| statistics/ |