Resource
| Id | Histone_ChIP-seq/ENCSR668NXG |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR668NXG [biosample_summary="Homo sapiens skeletal muscle tissue tissue male adult (54 years)" and target="H3K4me1"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (54 years) output_type: pseudoreplicated peaks audit_internal_action: Archived analysis {ENCAN904HCV|/analyses/ENCAN904HCV/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed redacted alignments file {ENCFF073VEQ|/files/ENCFF073VEQ/} processed by ChIP-seq ENCODE3 hg19 pipeline has 24726074 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 {ENCFF073VEQ|/files/ENCFF073VEQ/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.85. 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 {ENCFF073VEQ|/files/ENCFF073VEQ/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 6.76. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR668NXG | float |
Histone_ChIP-seq_ENCSR668NXG |
Histone_ChIP-seq ENCSR668NXG [biosample_summary="Homo sapiens skeletal muscle tissue tissue male adult (54 years)" and target="H3K4me1"]
|
 |
[1.53, 40.7] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 92768762 | 2.88% | 154229 |
| chr1 | 9802946 | 3.94% | 15678 |
| chr2 | 7301254 | 3.01% | 12176 |
| chr3 | 6059915 | 3.06% | 10121 |
| chr4 | 2773835 | 1.46% | 5087 |
| chr5 | 4415893 | 2.43% | 7612 |
| chr6 | 4681712 | 2.74% | 8470 |
| chr7 | 3991192 | 2.50% | 7056 |
| chr8 | 3574072 | 2.46% | 6196 |
| chr9 | 4264491 | 3.08% | 6751 |
| chr10 | 5214945 | 3.90% | 8522 |
| chr11 | 5406292 | 4.00% | 8588 |
| chr12 | 4062122 | 3.05% | 6762 |
| chr13 | 1671534 | 1.46% | 3233 |
| chr14 | 3065624 | 2.86% | 5013 |
| chr15 | 3416901 | 3.35% | 5702 |
| chr16 | 3927320 | 4.35% | 6290 |
| chr17 | 5619776 | 6.75% | 8387 |
| chr18 | 1723892 | 2.14% | 3119 |
| chr19 | 3749038 | 6.40% | 5857 |
| chr20 | 2947257 | 4.57% | 4788 |
| chr21 | 1066614 | 2.28% | 1836 |
| chr22 | 2880271 | 5.67% | 4229 |
| chrX | 1132441 | 0.73% | 2692 |
| chrY | 19425 | 0.03% | 64 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 154229 | 160 | 22523 | 601.5 | 417 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF617ELX.bed.gz | 3.01 MB | b247d822c0f2a4510826b6206b927636 |
| ENCFF617ELX.tabix.bed.gz | 1.45 MB | 63f0e0073787c4f71ed303cae9291496 |
| ENCFF617ELX.tabix.bed.gz.tbi | 321.16 KB | ce7bc67c159dbb5075dddbf1637b199e |
| genomic_resource.yaml | 3.29 KB | 6d7ccefad955562faba6f690e3e4a1e7 |
| statistics/ |