Resource
| Id | Histone_ChIP-seq/ENCSR768JED |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR768JED [biosample_summary="Homo sapiens OCI-LY1" and target="H3K9me2"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN242NZJ|/analyses/ENCAN242NZJ/} has in progress subobject document {243425e4-7b0c-4090-81a0-5d3f5d1bf8b7|/documents/243425e4-7b0c-4090-81a0-5d3f5d1bf8b7/} audit_internal_action: Released analysis {ENCAN242NZJ|/analyses/ENCAN242NZJ/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_warning: Processed alignments file {ENCFF539XDZ|/files/ENCFF539XDZ/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 38660894 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 {ENCFF539XDZ|/files/ENCFF539XDZ/} 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 {ENCFF539XDZ|/files/ENCFF539XDZ/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 6.33. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR768JED | float |
Histone_ChIP-seq_ENCSR768JED |
Histone_ChIP-seq ENCSR768JED [biosample_summary="Homo sapiens OCI-LY1" and target="H3K9me2"]
|
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[1.67, 4.22] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 557466 | 0.02% | 1632 |
| chr1 | 10091 | <0.01% | 33 |
| chr2 | 13951 | 0.01% | 45 |
| chr3 | 89476 | 0.05% | 260 |
| chr4 | 12703 | 0.01% | 43 |
| chr5 | 13124 | 0.01% | 43 |
| chr6 | 8048 | <0.01% | 28 |
| chr7 | 154385 | 0.10% | 427 |
| chr8 | 144167 | 0.10% | 409 |
| chr9 | 4739 | <0.01% | 14 |
| chr10 | 3711 | <0.01% | 13 |
| chr11 | 5651 | <0.01% | 19 |
| chr12 | 4866 | <0.01% | 17 |
| chr13 | 68632 | 0.06% | 207 |
| chr14 | 4761 | <0.01% | 17 |
| chr15 | 3901 | <0.01% | 12 |
| chr16 | 2199 | <0.01% | 5 |
| chr17 | 1200 | <0.01% | 4 |
| chr18 | 6626 | 0.01% | 21 |
| chr19 | 867 | <0.01% | 2 |
| chr20 | 374 | <0.01% | 1 |
| chr21 | 3227 | 0.01% | 9 |
| chr22 | 516 | <0.01% | 2 |
| chrX | 251 | <0.01% | 1 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 1632 | 208 | 1060 | 341.58 | 305 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF241SEE.bed.gz | 32.75 KB | 1023c8fc19805ccc8a7326ddd4972014 |
| ENCFF241SEE.tabix.bed.gz | 17.42 KB | 7a02d25a19072be3141e50ce9066529f |
| ENCFF241SEE.tabix.bed.gz.tbi | 19.05 KB | e867637904e2c65aeb32a14e1698c90a |
| genomic_resource.yaml | 3.47 KB | ebfb89153fef95ddf699bffa50431825 |
| statistics/ |
