Resource
| Id | Histone_ChIP-seq/ENCSR000AKV |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000AKV [biosample_summary="Homo sapiens K562" and target="H3K9ac"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN231GNS|/analyses/ENCAN231GNS/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_internal_action: Released analysis {ENCAN231GNS|/analyses/ENCAN231GNS/} has in progress subobject document {690a9496-862d-44ed-9d8c-9f83c807bdb6|/documents/690a9496-862d-44ed-9d8c-9f83c807bdb6/} audit_not_compliant: Processed alignments file {ENCFF505NMT|/files/ENCFF505NMT/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 8702063 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K9ac-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 {ENCFF149MXA|/files/ENCFF149MXA/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 13361217 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K9ac-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 {ENCFF505NMT|/files/ENCFF505NMT/} processed by ChIP-seq ENCODE4 v1.6.1 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 {ENCFF505NMT|/files/ENCFF505NMT/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 6.86. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000AKV | float |
Histone_ChIP-seq_ENCSR000AKV |
Histone_ChIP-seq ENCSR000AKV [biosample_summary="Homo sapiens K562" and target="H3K9ac"]
|
 |
[1.81, 98.8] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 49339542 | 1.53% | 38252 |
| chr1 | 5317712 | 2.14% | 4033 |
| chr2 | 3388316 | 1.40% | 2614 |
| chr3 | 2938458 | 1.48% | 2268 |
| chr4 | 1830678 | 0.96% | 1361 |
| chr5 | 2213715 | 1.22% | 1619 |
| chr6 | 3407100 | 1.99% | 2468 |
| chr7 | 2432437 | 1.53% | 1890 |
| chr8 | 1881051 | 1.30% | 1461 |
| chr9 | 1888259 | 1.36% | 1522 |
| chr10 | 2200861 | 1.64% | 1670 |
| chr11 | 2706802 | 2.00% | 2126 |
| chr12 | 2620831 | 1.97% | 2030 |
| chr13 | 782363 | 0.68% | 601 |
| chr14 | 1443265 | 1.35% | 1082 |
| chr15 | 1545089 | 1.51% | 1261 |
| chr16 | 1895719 | 2.10% | 1537 |
| chr17 | 2794530 | 3.36% | 2151 |
| chr18 | 704122 | 0.88% | 555 |
| chr19 | 2864726 | 4.89% | 2397 |
| chr20 | 1328706 | 2.06% | 1093 |
| chr21 | 554571 | 1.19% | 413 |
| chr22 | 1036509 | 2.04% | 852 |
| chrX | 1563722 | 1.00% | 1248 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 38252 | 203 | 13352 | 1289.86 | 887 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF891CHI.bed.gz | 1003.52 KB | 0c4d48de710e88b7049fe53eb9b31dbe |
| ENCFF891CHI.tabix.bed.gz | 430.99 KB | c8fa28e5c928deb0f481d8b7bebb6869 |
| ENCFF891CHI.tabix.bed.gz.tbi | 157.48 KB | ce3c2113478037246929860ff460baf7 |
| genomic_resource.yaml | 4.05 KB | ae0e6e3f001f526b4ac1abbdc8916d3a |
| statistics/ |