Resource
| Id | Histone_ChIP-seq/ENCSR906NGD |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR906NGD [biosample_summary="Homo sapiens GM23248" and target="H3K4me1"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN791ZZC|/analyses/ENCAN791ZZC/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_internal_action: Released analysis {ENCAN791ZZC|/analyses/ENCAN791ZZC/} has in progress subobject document {bc67edf6-d23c-49c4-9d7a-2a2a374eb09d|/documents/bc67edf6-d23c-49c4-9d7a-2a2a374eb09d/} audit_not_compliant: Processed alignments file {ENCFF515SNS|/files/ENCFF515SNS/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 29662258 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 {ENCFF718YCJ|/files/ENCFF718YCJ/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 31294435 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 {ENCFF515SNS|/files/ENCFF515SNS/} 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 {ENCFF515SNS|/files/ENCFF515SNS/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 9.26. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR906NGD | float |
Histone_ChIP-seq_ENCSR906NGD |
Histone_ChIP-seq ENCSR906NGD [biosample_summary="Homo sapiens GM23248" and target="H3K4me1"]
|
 |
[1.67, 11.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 150846927 | 4.69% | 136430 |
| chr1 | 14427577 | 5.80% | 12908 |
| chr2 | 13810401 | 5.70% | 12115 |
| chr3 | 11435771 | 5.77% | 10037 |
| chr4 | 8149372 | 4.28% | 7238 |
| chr5 | 9436260 | 5.20% | 8132 |
| chr6 | 9645688 | 5.65% | 8616 |
| chr7 | 7633883 | 4.79% | 6864 |
| chr8 | 7720412 | 5.32% | 6887 |
| chr9 | 6549041 | 4.73% | 5823 |
| chr10 | 7558363 | 5.65% | 6752 |
| chr11 | 7595953 | 5.62% | 6782 |
| chr12 | 8000137 | 6.00% | 7029 |
| chr13 | 4117772 | 3.60% | 3757 |
| chr14 | 4704361 | 4.39% | 4198 |
| chr15 | 5428310 | 5.32% | 4735 |
| chr16 | 3514061 | 3.89% | 3478 |
| chr17 | 5358156 | 6.44% | 5059 |
| chr18 | 3362986 | 4.18% | 3100 |
| chr19 | 2418593 | 4.13% | 2704 |
| chr20 | 3341791 | 5.19% | 3195 |
| chr21 | 1718623 | 3.68% | 1617 |
| chr22 | 2116223 | 4.16% | 2066 |
| chrX | 2661118 | 1.71% | 3162 |
| chrY | 142075 | 0.25% | 176 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 136430 | 200 | 22554 | 1105.67 | 873 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF314UFY.bed.gz | 3.37 MB | 0fb8571bb5f7a34c88885184305f8472 |
| ENCFF314UFY.tabix.bed.gz | 1.45 MB | 99549adfd076bd22a20d31809e4517d6 |
| ENCFF314UFY.tabix.bed.gz.tbi | 355.31 KB | 21fe0b296f2d7394909499d060acff33 |
| genomic_resource.yaml | 3.93 KB | 0df0b03197a94db9fd668fd7f6a796f0 |
| statistics/ |