Resource
| Id | Histone_ChIP-seq/ENCSR146JFX |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR146JFX [biosample_summary="Homo sapiens skeletal muscle tissue tissue" and target="H3K4me1"] |
| Description |
status: released biological_replicates: Rep 1 summary: output_type: pseudoreplicated peaks audit_internal_action: Archived analysis {ENCAN768LPH|/analyses/ENCAN768LPH/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed redacted alignments file {ENCFF614KUA|/files/ENCFF614KUA/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 15964936 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 redacted alignments file {ENCFF614KUA|/files/ENCFF614KUA/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.82. 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 {ENCFF614KUA|/files/ENCFF614KUA/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 5.63. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR146JFX | float |
Histone_ChIP-seq_ENCSR146JFX |
Histone_ChIP-seq ENCSR146JFX [biosample_summary="Homo sapiens skeletal muscle tissue tissue" and target="H3K4me1"]
|
 |
[1.98, 26.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 81526298 | 2.53% | 120306 |
| chr1 | 8675129 | 3.48% | 12238 |
| chr2 | 6650220 | 2.75% | 9921 |
| chr3 | 5585462 | 2.82% | 8366 |
| chr4 | 2759790 | 1.45% | 4464 |
| chr5 | 4099305 | 2.26% | 6337 |
| chr6 | 4417737 | 2.59% | 7001 |
| chr7 | 3438567 | 2.16% | 5403 |
| chr8 | 3227560 | 2.22% | 5113 |
| chr9 | 3801644 | 2.75% | 5416 |
| chr10 | 4583873 | 3.43% | 6662 |
| chr11 | 4605518 | 3.41% | 6553 |
| chr12 | 3779049 | 2.84% | 5541 |
| chr13 | 1592681 | 1.39% | 2696 |
| chr14 | 2761986 | 2.58% | 3989 |
| chr15 | 3000295 | 2.94% | 4424 |
| chr16 | 3148639 | 3.49% | 4446 |
| chr17 | 4633180 | 5.56% | 6164 |
| chr17_GL000205v2_random | 1559 | 0.84% | 2 |
| chr18 | 1503904 | 1.87% | 2385 |
| chr19 | 2957698 | 5.05% | 4014 |
| chr20 | 2496495 | 3.87% | 3515 |
| chr21 | 817386 | 1.75% | 1288 |
| chr22 | 2217334 | 4.36% | 2897 |
| chrX | 762506 | 0.49% | 1449 |
| chrY | 8781 | 0.02% | 22 |
| 3341 contigs with no values (128891494 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 120306 | 155 | 16597 | 677.66 | 518 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF291HWC.bed.gz | 2.35 MB | 323e50b95120c27a9f03133f5ba56838 |
| ENCFF291HWC.tabix.bed.gz | 1.15 MB | 74a0b1fd549e8b57418d051d88a15f87 |
| ENCFF291HWC.tabix.bed.gz.tbi | 300.41 KB | 8cc8f3de4bef194930a453e08af9f44e |
| genomic_resource.yaml | 3.27 KB | 395e25821e63af976a5a029a9d5d30f3 |
| statistics/ |