Resource
| Id | TF_ChIP-seq/ENCSR000ARD |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | TF_ChIP-seq ENCSR000ARD [biosample_summary="Homo sapiens GM12878" and target="EZH2"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: optimal IDR thresholded peaks audit_internal_action: Archived analysis {ENCAN652RAB|/analyses/ENCAN652RAB/} has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/} audit_not_compliant: Processed alignments file {ENCFF689FFZ|/files/ENCFF689FFZ/} processed by ChIP-seq ENCODE3 hg19 pipeline has 9635069 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting EZH2-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 {ENCFF689FFZ|/files/ENCFF689FFZ/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.82. 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 {ENCFF689FFZ|/files/ENCFF689FFZ/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 5.36. 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 {ENCFF385WMX|/files/ENCFF385WMX/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.83. 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 {ENCFF385WMX|/files/ENCFF385WMX/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 5.73. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF134RHC|/files/ENCFF134RHC/}, {ENCFF413QYZ|/files/ENCFF413QYZ/} processed by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 1.03 and a self consistency ratio of 3.83. According to ENCODE standards, having both rescue ratio and self consistency ratio values < 2 is recommended, but having only one of the ratio values < 2 is acceptable. audit_warning: Replicate concordance in ChIP-seq experiments is measured by calculating IDR values (Irreproducible Discovery Rate). ENCODE processed IDR thresholded peaks files {ENCFF437BUE|/files/ENCFF437BUE/}, {ENCFF678JII|/files/ENCFF678JII/} processed by ChIP-seq ENCODE3 hg19 pipeline have a rescue ratio of 1.03 and a self consistency ratio of 3.83. According to ENCODE standards, having both rescue ratio and self consistency ratio values < 2 is recommended, but having only one of the ratio values < 2 is acceptable. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| TF_ChIP-seq_ENCSR000ARD | float |
TF_ChIP-seq_ENCSR000ARD |
TF_ChIP-seq ENCSR000ARD [biosample_summary="Homo sapiens GM12878" and target="EZH2"]
|
 |
[7.54, 171] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 543705 | 0.02% | 2024 |
| chr1 | 63042 | 0.03% | 236 |
| chr2 | 51770 | 0.02% | 190 |
| chr3 | 33687 | 0.02% | 128 |
| chr4 | 24365 | 0.01% | 96 |
| chr5 | 28274 | 0.02% | 98 |
| chr6 | 46777 | 0.03% | 173 |
| chr7 | 34331 | 0.02% | 129 |
| chr8 | 20549 | 0.01% | 76 |
| chr9 | 21066 | 0.02% | 79 |
| chr10 | 33905 | 0.03% | 126 |
| chr11 | 30238 | 0.02% | 111 |
| chr12 | 30680 | 0.02% | 119 |
| chr13 | 11448 | 0.01% | 40 |
| chr14 | 15072 | 0.01% | 57 |
| chr15 | 16612 | 0.02% | 60 |
| chr16 | 8739 | 0.01% | 32 |
| chr17 | 35008 | 0.04% | 136 |
| chr18 | 7226 | 0.01% | 27 |
| chr19 | 11165 | 0.02% | 39 |
| chr20 | 7807 | 0.01% | 29 |
| chr21 | 3455 | 0.01% | 13 |
| chr22 | 5233 | 0.01% | 19 |
| chrX | 3256 | <0.01% | 11 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 2024 | 5 | 296 | 268.63 | 296 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF678JII.bed.gz | 36.32 KB | e89a61b52a33a3db505994d17393df9a |
| ENCFF678JII.tabix.bed.gz | 23.73 KB | e1bb8ff7e2740e0077006f1e2ca4db3d |
| ENCFF678JII.tabix.bed.gz.tbi | 18.88 KB | 887b76b40ac79d712bd4fce1fa65e19f |
| genomic_resource.yaml | 5.58 KB | 8def5103a4f4fc56a77ca09a54591c4d |
| statistics/ |