Resource
| Id | Histone_ChIP-seq/ENCSR004AKD |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR004AKD [biosample_summary="Homo sapiens mesenchymal stem cell female adult and female adult (41 years) and female adult (59 years), originated from adipose tissue" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: female adult (59 years) female adult female adult (41 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN696MOA|/analyses/ENCAN696MOA/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} 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 redacted alignments file {ENCFF208JXM|/files/ENCFF208JXM/} processed by ChIP-seq ENCODE4 v1.7.0 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 redacted alignments file {ENCFF208JXM|/files/ENCFF208JXM/} processed by ChIP-seq ENCODE4 v1.7.0 GRCh38 pipeline was generated from a library with PBC2 value of 7.35. 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 redacted alignments file {ENCFF600DDJ|/files/ENCFF600DDJ/} processed by ChIP-seq ENCODE4 v1.7.0 GRCh38 pipeline was generated from a library with PBC1 value of 0.84. 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 redacted alignments file {ENCFF600DDJ|/files/ENCFF600DDJ/} processed by ChIP-seq ENCODE4 v1.7.0 GRCh38 pipeline was generated from a library with PBC2 value of 6.66. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR004AKD | float |
Histone_ChIP-seq_ENCSR004AKD |
Histone_ChIP-seq ENCSR004AKD [biosample_summary="Homo sapiens mesenchymal stem cell female adult and female adult (41 years) and female adult (59 years), originated from adipose tissue" and target="H3K4me3"]
|
 |
[1.75, 76] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 76008222 | 2.36% | 67059 |
| chr1 | 7056424 | 2.83% | 6121 |
| chr2 | 5458850 | 2.25% | 5048 |
| chr3 | 4404068 | 2.22% | 3895 |
| chr4 | 3406512 | 1.79% | 3010 |
| chr5 | 3983065 | 2.19% | 3655 |
| chr6 | 4424781 | 2.59% | 3815 |
| chr7 | 3769025 | 2.37% | 3393 |
| chr8 | 3110805 | 2.14% | 2915 |
| chr9 | 3180236 | 2.30% | 2882 |
| chr10 | 3601180 | 2.69% | 3320 |
| chr11 | 3868951 | 2.86% | 3281 |
| chr12 | 4129298 | 3.10% | 3405 |
| chr13 | 1749613 | 1.53% | 1699 |
| chr14 | 2339751 | 2.19% | 2030 |
| chr15 | 2488019 | 2.44% | 2196 |
| chr16 | 2655649 | 2.94% | 2228 |
| chr17 | 3784890 | 4.55% | 3208 |
| chr18 | 1526236 | 1.90% | 1468 |
| chr19 | 5222620 | 8.91% | 4376 |
| chr20 | 1753484 | 2.72% | 1579 |
| chr21 | 845297 | 1.81% | 786 |
| chr22 | 1368156 | 2.69% | 1177 |
| chrX | 1881312 | 1.21% | 1572 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 67059 | 190 | 21289 | 1133.45 | 717 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF166VPJ.bed.gz | 1.71 MB | d3d0db413410de8a6ddc42849312aed1 |
| ENCFF166VPJ.tabix.bed.gz | 747.97 KB | 079975815200e118755263ecb8f1d2bd |
| ENCFF166VPJ.tabix.bed.gz.tbi | 288.22 KB | 13ddace9ac378b35ef32d9c023f88e66 |
| genomic_resource.yaml | 4.53 KB | c942741fe7ea53749bf6bb143d32d5c8 |
| statistics/ |