Resource
| Id | Histone_ChIP-seq/ENCSR558XOU |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR558XOU [biosample_summary="Homo sapiens iPS-15b" and target="H3K9me3"] |
| Description |
status: released biological_replicates: Rep 1 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN524QIH|/analyses/ENCAN524QIH/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_internal_action: Released analysis {ENCAN524QIH|/analyses/ENCAN524QIH/} has in progress subobject document {8c9d6cb3-72ef-4d26-9fdf-5f1f87f8a88f|/documents/8c9d6cb3-72ef-4d26-9fdf-5f1f87f8a88f/} audit_not_compliant: Processed unfiltered alignments file {ENCFF198HRF|/files/ENCFF198HRF/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 26731048 mapped reads. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K9me3-human and investigated as a broad histone mark is 35 million mapped reads. 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 {ENCFF229YIF|/files/ENCFF229YIF/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.89. 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 {ENCFF229YIF|/files/ENCFF229YIF/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 8.81. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR558XOU | float |
Histone_ChIP-seq_ENCSR558XOU |
Histone_ChIP-seq ENCSR558XOU [biosample_summary="Homo sapiens iPS-15b" and target="H3K9me3"]
|
 |
[2.07, 17] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 14885903 | 0.46% | 28845 |
| chr1 | 875147 | 0.35% | 1693 |
| chr2 | 749849 | 0.31% | 1452 |
| chr3 | 548475 | 0.28% | 1115 |
| chr4 | 712105 | 0.37% | 1352 |
| chr5 | 613935 | 0.34% | 1228 |
| chr6 | 569466 | 0.33% | 1177 |
| chr7 | 949414 | 0.60% | 1784 |
| chr8 | 885398 | 0.61% | 1732 |
| chr9 | 372952 | 0.27% | 696 |
| chr10 | 619692 | 0.46% | 1202 |
| chr11 | 613307 | 0.45% | 1240 |
| chr12 | 664466 | 0.50% | 1309 |
| chr13 | 351061 | 0.31% | 696 |
| chr14 | 560708 | 0.52% | 1074 |
| chr15 | 229331 | 0.22% | 452 |
| chr16 | 563150 | 0.62% | 982 |
| chr17 | 354670 | 0.43% | 629 |
| chr18 | 222564 | 0.28% | 440 |
| chr19 | 1556746 | 2.66% | 2603 |
| chr20 | 276172 | 0.43% | 527 |
| chr21 | 946414 | 2.03% | 1769 |
| chr22 | 289932 | 0.57% | 541 |
| chrX | 1355171 | 0.87% | 3134 |
| chrY | 5778 | 0.01% | 18 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 28845 | 170 | 10049 | 516.07 | 431 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF281GRX.bed.gz | 498.0 KB | 5b4ecdb22ee75039973d4f3acd3259b6 |
| ENCFF281GRX.tabix.bed.gz | 264.38 KB | e7d6b5ef7396cd139476c4889bcb931f |
| ENCFF281GRX.tabix.bed.gz.tbi | 133.62 KB | 4231972439e9a605b2f04487a2140646 |
| genomic_resource.yaml | 3.42 KB | 50b2334e3112c75967d091903bc2d5d0 |
| statistics/ |