Resource
| Id | Histone_ChIP-seq/ENCSR032FUX |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR032FUX [biosample_summary="Homo sapiens subcutaneous abdominal adipose tissue tissue nuclear fraction female adult (81 years)" and target="H3K4me1"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (81 years) nuclear fraction output_type: pseudoreplicated peaks audit_internal_action: Archived analysis {ENCAN264EJZ|/analyses/ENCAN264EJZ/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed redacted alignments file {ENCFF615BTE|/files/ENCFF615BTE/} processed by ChIP-seq ENCODE3 hg19 pipeline has 26357485 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 {ENCFF615BTE|/files/ENCFF615BTE/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.89. 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 {ENCFF615BTE|/files/ENCFF615BTE/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 9.26. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR032FUX | float |
Histone_ChIP-seq_ENCSR032FUX |
Histone_ChIP-seq ENCSR032FUX [biosample_summary="Homo sapiens subcutaneous abdominal adipose tissue tissue nuclear fraction female adult (81 years)" and target="H3K4me1"]
|
 |
[1.31, 44.1] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 146209833 | 4.54% | 160828 |
| chr1 | 14180910 | 5.70% | 15058 |
| chr2 | 11657104 | 4.81% | 13079 |
| chr3 | 9384639 | 4.73% | 10594 |
| chr4 | 4987860 | 2.62% | 6203 |
| chr5 | 7712747 | 4.25% | 8819 |
| chr6 | 7807508 | 4.57% | 9149 |
| chr7 | 6903625 | 4.33% | 8034 |
| chr8 | 6153390 | 4.24% | 7171 |
| chr9 | 6601611 | 4.77% | 7033 |
| chr10 | 7817264 | 5.84% | 8414 |
| chr11 | 8439843 | 6.25% | 8579 |
| chr12 | 7055546 | 5.29% | 7840 |
| chr13 | 3267316 | 2.86% | 3885 |
| chr14 | 4921797 | 4.60% | 5201 |
| chr15 | 5154992 | 5.05% | 5538 |
| chr16 | 5346343 | 5.92% | 5528 |
| chr17 | 7840089 | 9.42% | 7733 |
| chr18 | 2799570 | 3.48% | 3352 |
| chr19 | 5755771 | 9.82% | 5891 |
| chr20 | 4507045 | 6.99% | 4788 |
| chr21 | 1841903 | 3.94% | 2100 |
| chr22 | 3696192 | 7.27% | 3592 |
| chrM | 1007 | 6.08% | 2 |
| chrX | 2375434 | 1.52% | 3244 |
| chrY | 327 | <0.01% | 1 |
| 3341 contigs with no values (129060516 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 160828 | 190 | 35615 | 909.11 | 676 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF074FRO.bed.gz | 3.52 MB | c09ab86c15db0e38adbe6272db7ad08e |
| ENCFF074FRO.tabix.bed.gz | 1.62 MB | 02a33ce831fac6366bd5749301d4a159 |
| ENCFF074FRO.tabix.bed.gz.tbi | 369.93 KB | 02d25e89805f5a39ba25bdcc3ab4914a |
| genomic_resource.yaml | 3.43 KB | ee068cc4c378e8ca9e2b0b8560632a1c |
| statistics/ |