Resource
| Id | Histone_ChIP-seq/ENCSR399VPY |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR399VPY [biosample_summary="Homo sapiens MM.1S" and target="H3K9me2"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Released analysis {ENCAN192FIS|/analyses/ENCAN192FIS/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_internal_action: Released analysis {ENCAN192FIS|/analyses/ENCAN192FIS/} has in progress subobject document {71bafd26-75ef-4bcc-abd2-96f54e857129|/documents/71bafd26-75ef-4bcc-abd2-96f54e857129/} audit_not_compliant: Processed alignments file {ENCFF278ELC|/files/ENCFF278ELC/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 30546060 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K9me2-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 {ENCFF278ELC|/files/ENCFF278ELC/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.80. 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 {ENCFF278ELC|/files/ENCFF278ELC/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 4.77. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR399VPY | float |
Histone_ChIP-seq_ENCSR399VPY |
Histone_ChIP-seq ENCSR399VPY [biosample_summary="Homo sapiens MM.1S" and target="H3K9me2"]
|
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[1.83, 4.31] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 155390 | <0.01% | 518 |
| chr1 | 11584 | <0.01% | 38 |
| chr2 | 17202 | 0.01% | 61 |
| chr3 | 19472 | 0.01% | 61 |
| chr4 | 17304 | 0.01% | 57 |
| chr5 | 12621 | 0.01% | 45 |
| chr6 | 4781 | <0.01% | 17 |
| chr7 | 16638 | 0.01% | 57 |
| chr8 | 6122 | <0.01% | 20 |
| chr9 | 2815 | <0.01% | 11 |
| chr10 | 5742 | <0.01% | 19 |
| chr11 | 9327 | 0.01% | 29 |
| chr12 | 9871 | 0.01% | 33 |
| chr13 | 5425 | <0.01% | 17 |
| chr15 | 3535 | <0.01% | 9 |
| chr16 | 1826 | <0.01% | 6 |
| chr17 | 2478 | <0.01% | 8 |
| chr18 | 3123 | <0.01% | 11 |
| chr19 | 396 | <0.01% | 1 |
| chr20 | 2912 | <0.01% | 10 |
| chr21 | 1337 | <0.01% | 5 |
| chr22 | 275 | <0.01% | 1 |
| chrX | 604 | <0.01% | 2 |
| 3344 contigs with no values (293348218 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 518 | 178 | 814 | 299.98 | 287 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF564TPJ.bed.gz | 11.87 KB | b00fa21e3bdf420b2df5a54bc7f3b770 |
| ENCFF564TPJ.tabix.bed.gz | 5.78 KB | 4fa8ebdde585e07a7063c9cc222b8cd9 |
| ENCFF564TPJ.tabix.bed.gz.tbi | 9.71 KB | b92435da1d3cce91dcf4827b77d727e5 |
| genomic_resource.yaml | 3.41 KB | acc5cad7821f80071b815f9b68c549ac |
| statistics/ |
