Resource
| Id | Histone_ChIP-seq/ENCSR952GVX |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR952GVX [biosample_summary="Homo sapiens H1" and target="H3K9ac"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN133AOB|/analyses/ENCAN133AOB/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF912QYY|/files/ENCFF912QYY/} processed by ChIP-seq ENCODE3 hg19 pipeline has 9843958 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 {ENCFF330CZC|/files/ENCFF330CZC/} processed by ChIP-seq ENCODE3 hg19 pipeline has 11122914 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 {ENCFF912QYY|/files/ENCFF912QYY/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.84. 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 {ENCFF912QYY|/files/ENCFF912QYY/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 6.55. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR952GVX | float |
Histone_ChIP-seq_ENCSR952GVX |
Histone_ChIP-seq ENCSR952GVX [biosample_summary="Homo sapiens H1" and target="H3K9ac"]
|
 |
[2.01, 87.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 17826427 | 0.55% | 32179 |
| chr1 | 1835952 | 0.74% | 3248 |
| chr2 | 1194850 | 0.49% | 2053 |
| chr3 | 1030331 | 0.52% | 1786 |
| chr4 | 652771 | 0.34% | 1110 |
| chr5 | 859612 | 0.47% | 1474 |
| chr6 | 1073819 | 0.63% | 1800 |
| chr7 | 820659 | 0.52% | 1498 |
| chr8 | 631736 | 0.44% | 1162 |
| chr9 | 689304 | 0.50% | 1307 |
| chr10 | 699808 | 0.52% | 1318 |
| chr11 | 993077 | 0.74% | 1797 |
| chr12 | 952633 | 0.71% | 1655 |
| chr13 | 337513 | 0.30% | 610 |
| chr14 | 607788 | 0.57% | 1083 |
| chr15 | 559648 | 0.55% | 1037 |
| chr16 | 762543 | 0.84% | 1456 |
| chr17 | 1053839 | 1.27% | 1993 |
| chr18 | 265913 | 0.33% | 498 |
| chr19 | 1260684 | 2.15% | 2313 |
| chr20 | 495718 | 0.77% | 950 |
| chr21 | 164223 | 0.35% | 307 |
| chr22 | 413634 | 0.81% | 816 |
| chrX | 448790 | 0.29% | 880 |
| chrY | 21582 | 0.04% | 28 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 32179 | 160 | 4871 | 553.98 | 383 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF073SMR.bed.gz | 639.7 KB | cce9f78946367459350a34f93d2a105c |
| ENCFF073SMR.tabix.bed.gz | 322.49 KB | b8e56a50a8696f06f35259ba71e1dd94 |
| ENCFF073SMR.tabix.bed.gz.tbi | 150.7 KB | 65b4d83ed0459fc698aeba6b39169007 |
| genomic_resource.yaml | 3.64 KB | 7c13793662a873e3d845c99ff9fd68ef |
| statistics/ |