Resource
| Id | TF_ChIP-seq/ENCSR000BIQ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | TF_ChIP-seq ENCSR000BIQ [biosample_summary="Homo sapiens H1" and target="SIX5"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: optimal IDR thresholded peaks audit_internal_action: File {ENCFF644BNN|/files/ENCFF644BNN/} with status 'released' is derived from file {ENCFF419RSJ|/files/ENCFF419RSJ/} with status 'archived'. audit_internal_action: Archived analysis {ENCAN691IYV|/analyses/ENCAN691IYV/} has in progress subobject quality standard {encode3-tf-chip|/quality-standards/encode3-tf-chip/} audit_warning: Processed alignments file {ENCFF892YBG|/files/ENCFF892YBG/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 10956008 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting SIX5-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 {ENCFF588EKB|/files/ENCFF588EKB/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 13205788 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting SIX5-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 {ENCFF588EKB|/files/ENCFF588EKB/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.81. 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 {ENCFF588EKB|/files/ENCFF588EKB/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 5.17. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| TF_ChIP-seq_ENCSR000BIQ | float |
TF_ChIP-seq_ENCSR000BIQ |
TF_ChIP-seq ENCSR000BIQ [biosample_summary="Homo sapiens H1" and target="SIX5"]
|
 |
[3.9, 454] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 744062 | 0.02% | 3410 |
| chr1 | 69442 | 0.03% | 316 |
| chr2 | 47745 | 0.02% | 216 |
| chr3 | 39518 | 0.02% | 179 |
| chr4 | 26775 | 0.01% | 118 |
| chr5 | 32183 | 0.02% | 145 |
| chr6 | 36530 | 0.02% | 164 |
| chr7 | 32652 | 0.02% | 149 |
| chr8 | 26301 | 0.02% | 116 |
| chr9 | 29668 | 0.02% | 134 |
| chr10 | 24674 | 0.02% | 112 |
| chr11 | 37638 | 0.03% | 175 |
| chr12 | 37963 | 0.03% | 176 |
| chr13 | 10168 | 0.01% | 48 |
| chr14 | 23893 | 0.02% | 105 |
| chr15 | 18996 | 0.02% | 85 |
| chr16 | 40854 | 0.05% | 188 |
| chr17 | 36574 | 0.04% | 170 |
| chr18 | 12442 | 0.02% | 56 |
| chr19 | 91920 | 0.16% | 444 |
| chr20 | 27219 | 0.04% | 132 |
| chr21 | 3796 | 0.01% | 18 |
| chr22 | 14029 | 0.03% | 63 |
| chrM | 4720 | 28.49% | 20 |
| chrUn_KI270466v1 | 236 | 19.14% | 1 |
| chrUn_KI270467v1 | 472 | 12.04% | 2 |
| chrX | 17182 | 0.01% | 76 |
| chrY | 472 | <0.01% | 2 |
| 3339 contigs with no values (129055363 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 3410 | 3 | 433 | 218.2 | 236 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF644BNN.bed.gz | 56.85 KB | ef33160da1dbc7d345f7eb36065717f9 |
| ENCFF644BNN.tabix.bed.gz | 41.3 KB | 22e32f852430980d3e9e6eaf19673277 |
| ENCFF644BNN.tabix.bed.gz.tbi | 36.85 KB | 93ee0d8c94c192b416593740eeb76be0 |
| genomic_resource.yaml | 3.81 KB | d7c96b38e032d9f7882f889977ff41a6 |
| statistics/ |