Resource
| Id | TF_ChIP-seq/ENCSR000BKD |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | TF_ChIP-seq ENCSR000BKD [biosample_summary="Homo sapiens H1" and target="YY1"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: optimal IDR thresholded peaks audit_internal_action: Archived analysis {ENCAN851SJM|/analyses/ENCAN851SJM/} has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/} audit_internal_action: File {ENCFF509GYP|/files/ENCFF509GYP/} with status 'released' is derived from file {ENCFF419RSJ|/files/ENCFF419RSJ/} with status 'archived'. audit_warning: Processed alignments file {ENCFF972SQO|/files/ENCFF972SQO/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 10196179 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting YY1-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 {ENCFF972SQO|/files/ENCFF972SQO/} 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 {ENCFF972SQO|/files/ENCFF972SQO/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 8.24. 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 {ENCFF489EBO|/files/ENCFF489EBO/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.87. 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 {ENCFF489EBO|/files/ENCFF489EBO/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 7.75. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| TF_ChIP-seq_ENCSR000BKD | float |
TF_ChIP-seq_ENCSR000BKD |
TF_ChIP-seq ENCSR000BKD [biosample_summary="Homo sapiens H1" and target="YY1"]
|
 |
[5.62, 568] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 7919009 | 0.25% | 26427 |
| chr1 | 784453 | 0.32% | 2616 |
| chr1_KI270713v1_random | 330 | 0.81% | 1 |
| chr2 | 559219 | 0.23% | 1868 |
| chr3 | 472736 | 0.24% | 1564 |
| chr4 | 333435 | 0.18% | 1091 |
| chr5 | 435000 | 0.24% | 1436 |
| chr6 | 460612 | 0.27% | 1548 |
| chr7 | 419319 | 0.26% | 1397 |
| chr8 | 313027 | 0.22% | 1044 |
| chr9 | 342081 | 0.25% | 1121 |
| chr10 | 367772 | 0.27% | 1218 |
| chr11 | 449159 | 0.33% | 1514 |
| chr12 | 425846 | 0.32% | 1437 |
| chr13 | 176333 | 0.15% | 573 |
| chr14 | 255581 | 0.24% | 861 |
| chr15 | 258211 | 0.25% | 870 |
| chr16 | 296124 | 0.33% | 989 |
| chr17 | 401609 | 0.48% | 1351 |
| chr18 | 163506 | 0.20% | 541 |
| chr19 | 374577 | 0.64% | 1267 |
| chr20 | 246303 | 0.38% | 823 |
| chr21 | 68535 | 0.15% | 229 |
| chr22 | 173155 | 0.34% | 579 |
| chr22_KI270733v1_random | 330 | 0.18% | 1 |
| chrM | 6822 | 41.17% | 26 |
| chrX | 130884 | 0.08% | 446 |
| chrY | 4050 | 0.01% | 16 |
| 3339 contigs with no values (128839999 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 26427 | 2 | 1047 | 299.66 | 330 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF509GYP.bed.gz | 415.29 KB | 60a16f0e4b44bad618dd6a05511bde2d |
| ENCFF509GYP.tabix.bed.gz | 308.1 KB | e6e2421b824c6a802622043a65809bde |
| ENCFF509GYP.tabix.bed.gz.tbi | 176.63 KB | 4eea318f9d1ce6852be0951d34817344 |
| genomic_resource.yaml | 4.61 KB | 817b53c12e4c73e731b841043f540382 |
| statistics/ |