Resource
| Id | Histone_ChIP-seq/ENCSR011CSR |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR011CSR [biosample_summary="Homo sapiens NCI-H929" and target="H3K4me1"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN615YBZ|/analyses/ENCAN615YBZ/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF097EKR|/files/ENCFF097EKR/} processed by ChIP-seq ENCODE4 v1.8.1 GRCh38 pipeline has 25211425 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 {ENCFF617CAT|/files/ENCFF617CAT/} processed by ChIP-seq ENCODE4 v1.8.1 GRCh38 pipeline has 14837573 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 {ENCFF097EKR|/files/ENCFF097EKR/} processed by ChIP-seq ENCODE4 v1.8.1 GRCh38 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 alignments file {ENCFF097EKR|/files/ENCFF097EKR/} processed by ChIP-seq ENCODE4 v1.8.1 GRCh38 pipeline was generated from a library with PBC2 value of 6.56. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR011CSR | float |
Histone_ChIP-seq_ENCSR011CSR |
Histone_ChIP-seq ENCSR011CSR [biosample_summary="Homo sapiens NCI-H929" and target="H3K4me1"]
|
 |
[1.55, 12.4] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 104105734 | 3.24% | 101421 |
| chr1 | 10154225 | 4.08% | 9496 |
| chr2 | 9054086 | 3.74% | 8922 |
| chr3 | 8036148 | 4.05% | 7693 |
| chr4 | 6319694 | 3.32% | 6439 |
| chr5 | 8324336 | 4.59% | 7482 |
| chr6 | 6873979 | 4.02% | 6648 |
| chr7 | 5081015 | 3.19% | 5136 |
| chr8 | 6637349 | 4.57% | 5986 |
| chr9 | 4061844 | 2.93% | 4098 |
| chr10 | 4701250 | 3.51% | 4642 |
| chr11 | 5357928 | 3.97% | 4951 |
| chr12 | 4433483 | 3.33% | 4526 |
| chr13 | 753231 | 0.66% | 1067 |
| chr14 | 3577144 | 3.34% | 3442 |
| chr15 | 3613132 | 3.54% | 3441 |
| chr16 | 2859129 | 3.16% | 2888 |
| chr17 | 3360286 | 4.04% | 3355 |
| chr18 | 2780134 | 3.46% | 2696 |
| chr19 | 1633672 | 2.79% | 1834 |
| chr20 | 2239776 | 3.48% | 2051 |
| chr21 | 1102089 | 2.36% | 1121 |
| chr22 | 1459301 | 2.87% | 1496 |
| chrX | 1692503 | 1.08% | 2011 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 101421 | 210 | 18679 | 1026.47 | 799 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF664LXA.bed.gz | 2.43 MB | bbc1748077ebccc2865fe3b599f1c9bd |
| ENCFF664LXA.tabix.bed.gz | 1.07 MB | ba70a1a8ec7904f3dc5e9771042836c7 |
| ENCFF664LXA.tabix.bed.gz.tbi | 362.19 KB | 57282e0ccafcfdfb32cd25ce0ffbeaf3 |
| genomic_resource.yaml | 3.9 KB | 49e394427f508cad86b3e65504048af4 |
| statistics/ |