Resource
| Id | Histone_ChIP-seq/ENCSR000ANX |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000ANX [biosample_summary="Homo sapiens myotube originated from skeletal muscle myoblast" and target="H3K4me1"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: male adult (22 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN913NPU|/analyses/ENCAN913NPU/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_internal_action: Released analysis {ENCAN913NPU|/analyses/ENCAN913NPU/} has in progress subobject document {e9c526bc-5670-4445-b796-24a0ad21f910|/documents/e9c526bc-5670-4445-b796-24a0ad21f910/} audit_not_compliant: Processed alignments file {ENCFF457JXC|/files/ENCFF457JXC/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 8152869 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 {ENCFF579KAA|/files/ENCFF579KAA/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 12757006 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 {ENCFF579KAA|/files/ENCFF579KAA/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.86. 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 {ENCFF579KAA|/files/ENCFF579KAA/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC2 value of 7.18. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000ANX | float |
Histone_ChIP-seq_ENCSR000ANX |
Histone_ChIP-seq ENCSR000ANX [biosample_summary="Homo sapiens myotube originated from skeletal muscle myoblast" and target="H3K4me1"]
|
 |
[1.89, 16.2] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 75554033 | 2.35% | 110176 |
| chr1 | 7585328 | 3.05% | 10548 |
| chr2 | 6819417 | 2.82% | 9776 |
| chr3 | 5327523 | 2.69% | 7775 |
| chr4 | 3272129 | 1.72% | 5035 |
| chr5 | 4244956 | 2.34% | 6224 |
| chr6 | 4417559 | 2.59% | 6575 |
| chr7 | 3220200 | 2.02% | 4901 |
| chr8 | 3120696 | 2.15% | 4802 |
| chr9 | 3446509 | 2.49% | 5024 |
| chr10 | 4143042 | 3.10% | 5888 |
| chr11 | 4372962 | 3.24% | 6075 |
| chr12 | 3712918 | 2.79% | 5386 |
| chr13 | 2011011 | 1.76% | 3030 |
| chr14 | 2494167 | 2.33% | 3500 |
| chr15 | 3115170 | 3.05% | 4301 |
| chr16 | 2244897 | 2.48% | 3376 |
| chr17 | 3524871 | 4.23% | 4908 |
| chr18 | 1427965 | 1.78% | 2184 |
| chr19 | 1409803 | 2.41% | 2233 |
| chr20 | 1921857 | 2.98% | 2818 |
| chr21 | 1092013 | 2.34% | 1529 |
| chr22 | 1653353 | 3.25% | 2269 |
| chrX | 938072 | 0.60% | 1933 |
| chrY | 37615 | 0.07% | 86 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 110176 | 188 | 7575 | 685.76 | 551 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF615CKT.bed.gz | 2.38 MB | 8d5284f433c0c057cd9e94f9de025763 |
| ENCFF615CKT.tabix.bed.gz | 1.11 MB | c84002d678d159459f493cee7ff78122 |
| ENCFF615CKT.tabix.bed.gz.tbi | 338.56 KB | 842ef0d3b0269c0bbdcc9f2fede9d1cf |
| genomic_resource.yaml | 4.0 KB | 62d853046f540a6e7ed23ac39d72d13f |
| statistics/ |