Resource
| Id | Histone_ChIP-seq/ENCSR691CSS |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR691CSS [biosample_summary="Homo sapiens common myeloid progenitor, CD34-positive male adult (42 years)" and target="H3K4me1"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (42 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN667AFZ|/analyses/ENCAN667AFZ/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_internal_action: Released analysis {ENCAN667AFZ|/analyses/ENCAN667AFZ/} has in progress subobject document {2126e1dd-6ca9-4c36-ab54-d320f43b674d|/documents/2126e1dd-6ca9-4c36-ab54-d320f43b674d/} audit_not_compliant: Processed alignments file {ENCFF990AAG|/files/ENCFF990AAG/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 28948585 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 alignments file {ENCFF990AAG|/files/ENCFF990AAG/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.85. 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 {ENCFF990AAG|/files/ENCFF990AAG/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 6.72. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR691CSS | float |
Histone_ChIP-seq_ENCSR691CSS |
Histone_ChIP-seq ENCSR691CSS [biosample_summary="Homo sapiens common myeloid progenitor, CD34-positive male adult (42 years)" and target="H3K4me1"]
|
 |
[1.88, 39.3] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 141507792 | 4.40% | 175060 |
| chr1 | 13896119 | 5.58% | 16656 |
| chr2 | 10976641 | 4.53% | 13698 |
| chr3 | 9100410 | 4.59% | 11529 |
| chr4 | 5906220 | 3.11% | 7944 |
| chr5 | 6938656 | 3.82% | 8745 |
| chr6 | 8359079 | 4.89% | 10666 |
| chr7 | 7011658 | 4.40% | 8884 |
| chr8 | 5827895 | 4.02% | 7346 |
| chr9 | 6015856 | 4.35% | 7150 |
| chr10 | 6697956 | 5.01% | 8217 |
| chr11 | 7294003 | 5.40% | 8453 |
| chr12 | 7393242 | 5.55% | 8858 |
| chr13 | 3379114 | 2.95% | 4482 |
| chr14 | 4686644 | 4.38% | 5597 |
| chr15 | 4820784 | 4.73% | 5652 |
| chr16 | 4980499 | 5.51% | 5829 |
| chr17 | 7378386 | 8.86% | 8303 |
| chr18 | 2773674 | 3.45% | 3553 |
| chr19 | 5536735 | 9.45% | 6816 |
| chr20 | 4002338 | 6.21% | 4780 |
| chr21 | 1936456 | 4.15% | 2231 |
| chr22 | 3310550 | 6.51% | 3756 |
| chrX | 3165058 | 2.03% | 5649 |
| chrY | 119819 | 0.21% | 266 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 175060 | 135 | 26434 | 808.34 | 533 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF536UXR.bed.gz | 3.61 MB | 7ec831f79d7e346dac5520e7cea3eb43 |
| ENCFF536UXR.tabix.bed.gz | 1.71 MB | fb4d0ba3050c82b89072b4d5569090aa |
| ENCFF536UXR.tabix.bed.gz.tbi | 369.23 KB | 7aa82eedb137ef63fde6e33f267a59b0 |
| genomic_resource.yaml | 3.54 KB | f976ff9289fba7cfd690478ebac0b3d7 |
| statistics/ |