Resource
| Id | Histone_ChIP-seq/ENCSR000DWS |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000DWS [biosample_summary="Homo sapiens foreskin fibroblast male newborn" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: male newborn output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN051HKH|/analyses/ENCAN051HKH/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} 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 {ENCFF153HAO|/files/ENCFF153HAO/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.84. 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 {ENCFF153HAO|/files/ENCFF153HAO/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 7.03. 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 {ENCFF224YBG|/files/ENCFF224YBG/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.84. 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 {ENCFF224YBG|/files/ENCFF224YBG/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 7.06. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000DWS | float |
Histone_ChIP-seq_ENCSR000DWS |
Histone_ChIP-seq ENCSR000DWS [biosample_summary="Homo sapiens foreskin fibroblast male newborn" and target="H3K4me3"]
|
 |
[1.88, 110] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 41505669 | 1.29% | 38884 |
| chr1 | 4002686 | 1.61% | 3676 |
| chr1_KI270713v1_random | 509 | 1.25% | 1 |
| chr2 | 2889274 | 1.19% | 2763 |
| chr3 | 2464539 | 1.24% | 2226 |
| chr4 | 1759360 | 0.92% | 1578 |
| chr5 | 2063283 | 1.14% | 1848 |
| chr6 | 2587516 | 1.51% | 2274 |
| chr7 | 1978512 | 1.24% | 1849 |
| chr8 | 1610794 | 1.11% | 1531 |
| chr9 | 1707551 | 1.23% | 1702 |
| chr10 | 1788651 | 1.34% | 1701 |
| chr11 | 2189913 | 1.62% | 1968 |
| chr12 | 2311716 | 1.73% | 2049 |
| chr13 | 893526 | 0.78% | 881 |
| chr14 | 1325216 | 1.24% | 1182 |
| chr15 | 1383846 | 1.36% | 1300 |
| chr16 | 1547437 | 1.71% | 1554 |
| chr17 | 2257699 | 2.71% | 2193 |
| chr17_GL000205v2_random | 1852 | 1.00% | 3 |
| chr18 | 769597 | 0.96% | 799 |
| chr19 | 2389635 | 4.08% | 2356 |
| chr20 | 1011927 | 1.57% | 990 |
| chr21 | 411319 | 0.88% | 401 |
| chr22 | 840502 | 1.65% | 835 |
| chr22_KI270733v1_random | 241 | 0.13% | 1 |
| chrUn_GL000195v1 | 306 | 0.17% | 2 |
| chrUn_GL000219v1 | 2231 | 1.24% | 4 |
| chrUn_GL000220v1 | 243 | 0.15% | 1 |
| chrX | 1268256 | 0.81% | 1192 |
| chrY | 47532 | 0.08% | 24 |
| 3336 contigs with no values (128147081 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 38884 | 140 | 30880 | 1067.42 | 616 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF111YIF.bed.gz | 981.68 KB | 31ec7fd8f57f4d50fb0d2ad02b92bd9c |
| ENCFF111YIF.tabix.bed.gz | 431.73 KB | f2bcd7d22eb34302fd985e027e8d033f |
| ENCFF111YIF.tabix.bed.gz.tbi | 185.36 KB | 11b66f09753f3f04675694115b6b4feb |
| genomic_resource.yaml | 4.26 KB | c289b219de44b932a34d0d246430a85f |
| statistics/ |