Resource
| Id | TF_ChIP-seq/ENCSR000BKC |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | TF_ChIP-seq ENCSR000BKC [biosample_summary="Homo sapiens H1" and target="ATF3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: IDR thresholded peaks audit_internal_action: Released analysis {ENCAN287LIV|/analyses/ENCAN287LIV/} has in progress subobject quality standard {encode4-tf-chip|/quality-standards/encode4-tf-chip/} audit_internal_action: Released analysis {ENCAN287LIV|/analyses/ENCAN287LIV/} has in progress subobject document {4c06f462-a5a8-42d1-8dc8-1b6d2fbf69be|/documents/4c06f462-a5a8-42d1-8dc8-1b6d2fbf69be/} audit_not_compliant: Processed alignments file {ENCFF149WSI|/files/ENCFF149WSI/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 9501309 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting ATF3-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: Processed alignments file {ENCFF061OVT|/files/ENCFF061OVT/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 12430546 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting ATF3-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 {ENCFF061OVT|/files/ENCFF061OVT/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 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 alignments file {ENCFF061OVT|/files/ENCFF061OVT/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 8.56. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| TF_ChIP-seq_ENCSR000BKC | float |
TF_ChIP-seq_ENCSR000BKC |
TF_ChIP-seq ENCSR000BKC [biosample_summary="Homo sapiens H1" and target="ATF3"]
|
 |
[3.64, 438] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 1295194 | 0.04% | 5569 |
| chr1 | 126855 | 0.05% | 548 |
| chr2 | 80597 | 0.03% | 343 |
| chr3 | 72754 | 0.04% | 313 |
| chr4 | 46590 | 0.02% | 200 |
| chr5 | 58699 | 0.03% | 251 |
| chr6 | 61731 | 0.04% | 267 |
| chr7 | 59942 | 0.04% | 258 |
| chr8 | 46284 | 0.03% | 196 |
| chr9 | 56248 | 0.04% | 242 |
| chr10 | 48093 | 0.04% | 207 |
| chr11 | 73820 | 0.05% | 317 |
| chr12 | 74821 | 0.06% | 319 |
| chr13 | 26226 | 0.02% | 110 |
| chr14 | 45924 | 0.04% | 196 |
| chr15 | 36178 | 0.04% | 155 |
| chr16 | 69744 | 0.08% | 303 |
| chr17 | 84337 | 0.10% | 370 |
| chr18 | 17599 | 0.02% | 77 |
| chr19 | 99270 | 0.17% | 428 |
| chr20 | 44976 | 0.07% | 194 |
| chr21 | 12831 | 0.03% | 54 |
| chr22 | 31161 | 0.06% | 133 |
| chrX | 19794 | 0.01% | 85 |
| chrY | 720 | <0.01% | 3 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 5569 | 6 | 388 | 232.57 | 240 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF440FTA.bed.gz | 89.77 KB | fe0c85937f9235e167d4fc3b2f6650ab |
| ENCFF440FTA.tabix.bed.gz | 66.16 KB | e639a38c10b3d86f297ecd4157940036 |
| ENCFF440FTA.tabix.bed.gz.tbi | 55.07 KB | bc845b4024ccc40b3ab506f8b7ab4ec2 |
| genomic_resource.yaml | 3.87 KB | 464fff7337933d7da259d137ccca3045 |
| statistics/ |