Resource
| Id | Histone_ChIP-seq/ENCSR000AOX |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000AOX [biosample_summary="Homo sapiens GM12878" and target="H3K9me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN588DXB|/analyses/ENCAN588DXB/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed unfiltered alignments file {ENCFF030QXS|/files/ENCFF030QXS/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 17550791 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_not_compliant: Processed unfiltered alignments file {ENCFF335MWA|/files/ENCFF335MWA/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 14579068 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 {ENCFF758GUH|/files/ENCFF758GUH/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.87. 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 {ENCFF758GUH|/files/ENCFF758GUH/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 7.50. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000AOX | float |
Histone_ChIP-seq_ENCSR000AOX |
Histone_ChIP-seq ENCSR000AOX [biosample_summary="Homo sapiens GM12878" and target="H3K9me3"]
|
 |
[1.78, 11.8] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 4666855 | 0.15% | 18835 |
| chr1 | 332148 | 0.13% | 1360 |
| chr1_KI270713v1_random | 158 | 0.39% | 1 |
| chr2 | 415712 | 0.17% | 1741 |
| chr3 | 381323 | 0.19% | 1576 |
| chr4 | 216638 | 0.11% | 948 |
| chr5 | 254808 | 0.14% | 1069 |
| chr6 | 306850 | 0.18% | 1288 |
| chr7 | 294962 | 0.19% | 1172 |
| chr8 | 214118 | 0.15% | 849 |
| chr9 | 149153 | 0.11% | 614 |
| chr10 | 212149 | 0.16% | 871 |
| chr11 | 156817 | 0.12% | 622 |
| chr12 | 342601 | 0.26% | 1259 |
| chr13 | 119478 | 0.10% | 518 |
| chr14 | 152880 | 0.14% | 601 |
| chr15 | 131428 | 0.13% | 531 |
| chr16 | 126581 | 0.14% | 450 |
| chr17 | 110872 | 0.13% | 440 |
| chr17_KI270729v1_random | 1057 | 0.38% | 3 |
| chr18 | 118123 | 0.15% | 466 |
| chr19 | 423168 | 0.72% | 1561 |
| chr20 | 57187 | 0.09% | 244 |
| chr21 | 51909 | 0.11% | 213 |
| chr22 | 36016 | 0.07% | 155 |
| chr22_KI270736v1_random | 135 | 0.07% | 1 |
| chrUn_GL000216v2 | 575 | 0.33% | 2 |
| chrUn_GL000224v1 | 206 | 0.11% | 1 |
| chrUn_KI270336v1 | 203 | 19.79% | 1 |
| chrX | 59466 | 0.04% | 277 |
| chrY | 134 | <0.01% | 1 |
| 3336 contigs with no values (128216254 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 18835 | 120 | 4035 | 247.78 | 196 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF218YZR.bed.gz | 322.47 KB | 19d7696f509a79059010733b8e78cfd6 |
| ENCFF218YZR.tabix.bed.gz | 178.73 KB | 08ccb71dc33345fa74d38c47c94f1025 |
| ENCFF218YZR.tabix.bed.gz.tbi | 86.57 KB | 2788db0e3f1f260efc3d987d7e677af7 |
| genomic_resource.yaml | 3.68 KB | ade9250cfdb5130b0472bca6639cbcfc |
| statistics/ |