Resource
| Id | Histone_ChIP-seq/ENCSR081JRM |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR081JRM [biosample_summary="Homo sapiens trophoblast cell originated from H1" and target="H3K18ac"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: male embryo output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN456BPM|/analyses/ENCAN456BPM/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_warning: Processed alignments file {ENCFF353QYE|/files/ENCFF353QYE/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 19777253 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K18ac-human and investigated as a transcription factor is 10 million usable fragments. The recommended value is > 20 million, but > 10 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 {ENCFF353QYE|/files/ENCFF353QYE/} 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 {ENCFF353QYE|/files/ENCFF353QYE/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 8.90. 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 {ENCFF022ZHL|/files/ENCFF022ZHL/} processed by ChIP-seq ENCODE3 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 {ENCFF022ZHL|/files/ENCFF022ZHL/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 8.01. 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 {ENCFF908OHX|/files/ENCFF908OHX/} processed by ChIP-seq ENCODE3 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 {ENCFF908OHX|/files/ENCFF908OHX/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 8.01. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR081JRM | float |
Histone_ChIP-seq_ENCSR081JRM |
Histone_ChIP-seq ENCSR081JRM [biosample_summary="Homo sapiens trophoblast cell originated from H1" and target="H3K18ac"]
|
 |
[1.68, 20.2] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 24481002 | 0.76% | 75082 |
| chr1 | 2601407 | 1.04% | 7859 |
| chr2 | 1694622 | 0.70% | 5348 |
| chr3 | 1298988 | 0.66% | 4095 |
| chr4 | 762170 | 0.40% | 2513 |
| chr5 | 1194254 | 0.66% | 3708 |
| chr6 | 1103063 | 0.65% | 3530 |
| chr7 | 1136230 | 0.71% | 3603 |
| chr8 | 1007540 | 0.69% | 3175 |
| chr9 | 1258816 | 0.91% | 3757 |
| chr10 | 1312325 | 0.98% | 4003 |
| chr11 | 1363718 | 1.01% | 4114 |
| chr12 | 1118872 | 0.84% | 3382 |
| chr13 | 527805 | 0.46% | 1725 |
| chr14 | 835261 | 0.78% | 2535 |
| chr15 | 825229 | 0.81% | 2512 |
| chr16 | 1051269 | 1.16% | 3109 |
| chr17 | 1503196 | 1.81% | 4374 |
| chr18 | 464445 | 0.58% | 1533 |
| chr19 | 1329205 | 2.27% | 3849 |
| chr20 | 764593 | 1.19% | 2275 |
| chr21 | 274964 | 0.59% | 839 |
| chr22 | 689518 | 1.36% | 2055 |
| chrUn_GL000195v1 | 174 | 0.10% | 1 |
| chrX | 350759 | 0.22% | 1148 |
| chrY | 12579 | 0.02% | 40 |
| 3341 contigs with no values (128894189 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 75082 | 135 | 3184 | 326.06 | 256 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF589PLG.bed.gz | 1.6 MB | 81e04b92d358fff9801c239825aaa24e |
| ENCFF589PLG.tabix.bed.gz | 767.79 KB | 413f0910de77d6b58d044535cb259905 |
| ENCFF589PLG.tabix.bed.gz.tbi | 222.82 KB | 05e699bbd45475cd47ab99d709ffdb28 |
| genomic_resource.yaml | 5.72 KB | 20a6932557e7c8c3e04d40a09b404242 |
| statistics/ |