Resource
| Id | Histone_ChIP-seq/ENCSR276ZBE |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR276ZBE [biosample_summary="Homo sapiens iPS-15b" and target="H3K4me1"] |
| Description |
status: released biological_replicates: Rep 1 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN479IUT|/analyses/ENCAN479IUT/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_internal_action: Released analysis {ENCAN479IUT|/analyses/ENCAN479IUT/} has in progress subobject document {c7b5e400-c3f1-40d2-a310-0fb6bc013b47|/documents/c7b5e400-c3f1-40d2-a310-0fb6bc013b47/} audit_not_compliant: Processed alignments file {ENCFF281EGX|/files/ENCFF281EGX/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 24753894 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me1-human and investigated as a broad histone mark is 20 million usable fragments. The recommended value is > 45 million, but > 35 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 {ENCFF281EGX|/files/ENCFF281EGX/} 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 {ENCFF281EGX|/files/ENCFF281EGX/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 9.08. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR276ZBE | float |
Histone_ChIP-seq_ENCSR276ZBE |
Histone_ChIP-seq ENCSR276ZBE [biosample_summary="Homo sapiens iPS-15b" and target="H3K4me1"]
|
 |
[1.84, 15.2] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 64037732 | 1.99% | 131264 |
| chr1 | 6014268 | 2.42% | 11833 |
| chr2 | 5194860 | 2.14% | 10546 |
| chr3 | 4745845 | 2.39% | 9555 |
| chr4 | 3467354 | 1.82% | 7076 |
| chr5 | 3867174 | 2.13% | 7801 |
| chr6 | 4182175 | 2.45% | 8364 |
| chr7 | 3394716 | 2.13% | 6900 |
| chr8 | 2934582 | 2.02% | 6014 |
| chr9 | 2706309 | 1.96% | 5474 |
| chr10 | 3004050 | 2.25% | 6154 |
| chr11 | 3141685 | 2.33% | 6517 |
| chr12 | 3174689 | 2.38% | 6530 |
| chr13 | 1871498 | 1.64% | 3808 |
| chr14 | 1998853 | 1.87% | 4112 |
| chr15 | 2202092 | 2.16% | 4382 |
| chr16 | 1765140 | 1.95% | 3883 |
| chr17 | 2193827 | 2.63% | 4791 |
| chr18 | 1623751 | 2.02% | 3303 |
| chr19 | 1075346 | 1.83% | 2732 |
| chr20 | 1544599 | 2.40% | 3244 |
| chr21 | 612681 | 1.31% | 1289 |
| chr22 | 997754 | 1.96% | 2129 |
| chrX | 2324484 | 1.49% | 4827 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 131264 | 170 | 5622 | 487.85 | 396 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF945ZPG.bed.gz | 2.44 MB | 0237636a23eb3ff7a7a9a950e65f8061 |
| ENCFF945ZPG.tabix.bed.gz | 1.24 MB | aee4b32eac438c76b4e424d8ba21ba75 |
| ENCFF945ZPG.tabix.bed.gz.tbi | 430.05 KB | 640bc423dbf291e3442f9f88e57bdfbd |
| genomic_resource.yaml | 3.42 KB | 7eefcce852ed69dbba956cb4190b9d47 |
| statistics/ |