Resource
| Id | Histone_ChIP-seq/ENCSR000ANY |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000ANY [biosample_summary="Homo sapiens myotube originated from skeletal muscle myoblast" and target="H3K4me2"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: male adult (22 years) output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN867UEU|/analyses/ENCAN867UEU/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF769PUA|/files/ENCFF769PUA/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 8865773 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me2-human and investigated as a narrow histone mark 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 {ENCFF428BQL|/files/ENCFF428BQL/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 10749468 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me2-human and investigated as a narrow histone mark 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 {ENCFF428BQL|/files/ENCFF428BQL/} processed by ChIP-seq ENCODE3 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 {ENCFF428BQL|/files/ENCFF428BQL/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 8.72. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000ANY | float |
Histone_ChIP-seq_ENCSR000ANY |
Histone_ChIP-seq ENCSR000ANY [biosample_summary="Homo sapiens myotube originated from skeletal muscle myoblast" and target="H3K4me2"]
|
 |
[1.81, 38.3] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 76318460 | 2.37% | 82858 |
| chr1 | 7218361 | 2.90% | 7754 |
| chr1_KI270713v1_random | 347 | 0.85% | 1 |
| chr2 | 6240815 | 2.58% | 6820 |
| chr3 | 5020139 | 2.53% | 5393 |
| chr4 | 3732581 | 1.96% | 4026 |
| chr5 | 4109124 | 2.26% | 4450 |
| chr6 | 4952297 | 2.90% | 5329 |
| chr7 | 3544964 | 2.22% | 4015 |
| chr8 | 3203278 | 2.21% | 3619 |
| chr9 | 3242349 | 2.34% | 3518 |
| chr10 | 3818545 | 2.85% | 4138 |
| chr11 | 3972975 | 2.94% | 4193 |
| chr12 | 4049560 | 3.04% | 4226 |
| chr13 | 2096456 | 1.83% | 2358 |
| chr14 | 2442907 | 2.28% | 2638 |
| chr15 | 2623743 | 2.57% | 2883 |
| chr16 | 2354206 | 2.61% | 2531 |
| chr17 | 3516632 | 4.22% | 3682 |
| chr17_GL000205v2_random | 2071 | 1.12% | 2 |
| chr18 | 1487579 | 1.85% | 1669 |
| chr19 | 2695602 | 4.60% | 2716 |
| chr20 | 1755097 | 2.72% | 1995 |
| chr21 | 955589 | 2.05% | 1074 |
| chr22 | 1394095 | 2.74% | 1490 |
| chrUn_GL000195v1 | 1652 | 0.90% | 3 |
| chrUn_GL000219v1 | 5008 | 2.79% | 5 |
| chrX | 1822914 | 1.17% | 2255 |
| chrY | 59574 | 0.10% | 75 |
| 3338 contigs with no values (128488655 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 82858 | 195 | 18258 | 921.08 | 674 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF856JNQ.bed.gz | 2.0 MB | f3a026c816e335199d83397021a83908 |
| ENCFF856JNQ.tabix.bed.gz | 901.57 KB | 57b09226df30b82bb9d5a0702a90a4cb |
| ENCFF856JNQ.tabix.bed.gz.tbi | 328.62 KB | e4452a9d4f3db89f4336445fd8c39d5a |
| genomic_resource.yaml | 3.75 KB | ed56efc0808d167318e6f78761f26713 |
| statistics/ |