Resource
| Id | Histone_ChIP-seq/ENCSR888OSH |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR888OSH [biosample_summary="Homo sapiens HUES48" and target="H3K4me1"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN332VZR|/analyses/ENCAN332VZR/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_internal_action: Released analysis {ENCAN332VZR|/analyses/ENCAN332VZR/} has in progress subobject document {342c0e6e-6108-4a76-aea3-e9a953e76d8d|/documents/342c0e6e-6108-4a76-aea3-e9a953e76d8d/} audit_not_compliant: Processed alignments file {ENCFF462OBO|/files/ENCFF462OBO/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 26439629 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_not_compliant: Processed alignments file {ENCFF577NII|/files/ENCFF577NII/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 31471884 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 {ENCFF462OBO|/files/ENCFF462OBO/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.90. 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 {ENCFF462OBO|/files/ENCFF462OBO/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 9.62. 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 {ENCFF577NII|/files/ENCFF577NII/} processed by ChIP-seq ENCODE4 v1.6.1 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 {ENCFF577NII|/files/ENCFF577NII/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 7.74. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR888OSH | float |
Histone_ChIP-seq_ENCSR888OSH |
Histone_ChIP-seq ENCSR888OSH [biosample_summary="Homo sapiens HUES48" and target="H3K4me1"]
|
 |
[1.6, 15.1] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 156426265 | 4.86% | 185253 |
| chr1 | 13387474 | 5.38% | 16001 |
| chr2 | 13250562 | 5.47% | 15456 |
| chr3 | 11734189 | 5.92% | 13445 |
| chr4 | 9445000 | 4.97% | 11075 |
| chr5 | 9668031 | 5.33% | 11148 |
| chr6 | 10330178 | 6.05% | 11849 |
| chr7 | 8759215 | 5.50% | 10209 |
| chr8 | 7631121 | 5.26% | 8975 |
| chr9 | 6597534 | 4.77% | 7762 |
| chr10 | 7322695 | 5.47% | 8573 |
| chr11 | 7580878 | 5.61% | 9029 |
| chr12 | 7652403 | 5.74% | 9158 |
| chr13 | 5137448 | 4.49% | 5954 |
| chr14 | 4765112 | 4.45% | 5748 |
| chr15 | 4935025 | 4.84% | 5772 |
| chr16 | 4009721 | 4.44% | 5026 |
| chr17 | 4690576 | 5.63% | 6039 |
| chr18 | 4339281 | 5.40% | 4941 |
| chr19 | 2057973 | 3.51% | 3134 |
| chr20 | 3325158 | 5.16% | 4128 |
| chr21 | 1625346 | 3.48% | 1958 |
| chr22 | 2093572 | 4.12% | 2656 |
| chrX | 6087773 | 3.90% | 7217 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 185253 | 173 | 15440 | 844.39 | 647 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF380SRX.bed.gz | 4.15 MB | cf0ddeb5c32e5c74d595d2f72cb08114 |
| ENCFF380SRX.tabix.bed.gz | 1.89 MB | 3222d4916ba4ed922743cdd153ec42fe |
| ENCFF380SRX.tabix.bed.gz.tbi | 505.13 KB | af9050425b737bec5fca22b8d10bc2e6 |
| genomic_resource.yaml | 5.24 KB | 93352ed91a0558bae60b1f5531a43dfa |
| statistics/ |