Resource
| Id | TF_ChIP-seq/ENCSR000BMO |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | TF_ChIP-seq ENCSR000BMO [biosample_summary="Homo sapiens HepG2" and target="FOXA1"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: optimal IDR thresholded peaks audit_internal_action: Archived analysis {ENCAN054ANI|/analyses/ENCAN054ANI/} has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/} audit_internal_action: File {ENCFF152BOT|/files/ENCFF152BOT/} with status 'released' is derived from file {ENCFF419RSJ|/files/ENCFF419RSJ/} with status 'archived'. audit_not_compliant: Processed alignments file {ENCFF332SRJ|/files/ENCFF332SRJ/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 9008536 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting FOXA1-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 {ENCFF401YVR|/files/ENCFF401YVR/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 15245612 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting FOXA1-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 {ENCFF401YVR|/files/ENCFF401YVR/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.86. 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 {ENCFF401YVR|/files/ENCFF401YVR/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 7.18. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| TF_ChIP-seq_ENCSR000BMO | float |
TF_ChIP-seq_ENCSR000BMO |
TF_ChIP-seq ENCSR000BMO [biosample_summary="Homo sapiens HepG2" and target="FOXA1"]
|
 |
[3.71, 561] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 12343307 | 0.38% | 49312 |
| chr1 | 1032142 | 0.41% | 4159 |
| chr1_KI270713v1_random | 284 | 0.70% | 1 |
| chr2 | 1335814 | 0.55% | 5311 |
| chr3 | 810403 | 0.41% | 3218 |
| chr4 | 538664 | 0.28% | 2150 |
| chr5 | 612274 | 0.34% | 2447 |
| chr6 | 952661 | 0.56% | 3769 |
| chr7 | 588476 | 0.37% | 2356 |
| chr8 | 524512 | 0.36% | 2099 |
| chr9 | 480633 | 0.35% | 1928 |
| chr10 | 566712 | 0.42% | 2270 |
| chr11 | 520138 | 0.39% | 2091 |
| chr12 | 549715 | 0.41% | 2185 |
| chr13 | 272162 | 0.24% | 1090 |
| chr14 | 458610 | 0.43% | 1832 |
| chr15 | 350810 | 0.34% | 1398 |
| chr16 | 517594 | 0.57% | 2072 |
| chr17 | 609301 | 0.73% | 2443 |
| chr18 | 264887 | 0.33% | 1061 |
| chr19 | 302265 | 0.52% | 1207 |
| chr20 | 486145 | 0.75% | 1946 |
| chr21 | 114523 | 0.25% | 463 |
| chr22 | 215604 | 0.42% | 856 |
| chrM | 2432 | 14.68% | 11 |
| chrUn_GL000195v1 | 284 | 0.16% | 1 |
| chrUn_GL000219v1 | 284 | 0.16% | 1 |
| chrX | 233230 | 0.15% | 936 |
| chrY | 2748 | <0.01% | 11 |
| 3338 contigs with no values (128657677 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 49312 | 1 | 811 | 250.31 | 284 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF152BOT.bed.gz | 824.57 KB | 1faa3c11f60f906af93089660d86ec97 |
| ENCFF152BOT.tabix.bed.gz | 572.73 KB | 02390aa0da15ae51280cc71dfac1fc48 |
| ENCFF152BOT.tabix.bed.gz.tbi | 265.42 KB | 898098e7886231f7d815d3314e9e8e9e |
| genomic_resource.yaml | 3.83 KB | 5ee1e454ce814a07ba974ced7817631e |
| statistics/ |