Resource
| Id | Histone_ChIP-seq/ENCSR521GRK |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR521GRK [biosample_summary="Homo sapiens PC-9" and target="H3K9me2"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN055IFT|/analyses/ENCAN055IFT/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF332SLT|/files/ENCFF332SLT/} processed by ChIP-seq ENCODE4 v1.8.1 GRCh38 pipeline has 31625868 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_not_compliant: Processed alignments file {ENCFF185YPL|/files/ENCFF185YPL/} processed by ChIP-seq ENCODE4 v1.8.1 GRCh38 pipeline has 24632349 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 {ENCFF185YPL|/files/ENCFF185YPL/} processed by ChIP-seq ENCODE4 v1.8.1 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 {ENCFF185YPL|/files/ENCFF185YPL/} processed by ChIP-seq ENCODE4 v1.8.1 GRCh38 pipeline was generated from a library with PBC2 value of 7.68. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR521GRK | float |
Histone_ChIP-seq_ENCSR521GRK |
Histone_ChIP-seq ENCSR521GRK [biosample_summary="Homo sapiens PC-9" and target="H3K9me2"]
|
 |
[1.49, 4.35] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 4542830 | 0.14% | 10215 |
| chr1 | 521677 | 0.21% | 1173 |
| chr2 | 454761 | 0.19% | 1035 |
| chr3 | 519967 | 0.26% | 1157 |
| chr4 | 108972 | 0.06% | 253 |
| chr5 | 461716 | 0.25% | 1017 |
| chr6 | 398879 | 0.23% | 871 |
| chr7 | 410185 | 0.26% | 913 |
| chr8 | 199663 | 0.14% | 450 |
| chr9 | 91449 | 0.07% | 215 |
| chr10 | 133588 | 0.10% | 299 |
| chr11 | 288730 | 0.21% | 659 |
| chr12 | 252462 | 0.19% | 579 |
| chr13 | 184133 | 0.16% | 410 |
| chr14 | 68898 | 0.06% | 166 |
| chr15 | 29648 | 0.03% | 68 |
| chr16 | 42461 | 0.05% | 103 |
| chr17 | 55977 | 0.07% | 124 |
| chr18 | 88448 | 0.11% | 193 |
| chr19 | 15029 | 0.03% | 36 |
| chr20 | 75239 | 0.12% | 175 |
| chr21 | 4606 | 0.01% | 14 |
| chr22 | 12336 | 0.02% | 28 |
| chrX | 124006 | 0.08% | 277 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 10215 | 213 | 1477 | 444.72 | 407 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF850NAU.bed.gz | 233.68 KB | c90418d4660d37cd9d9c5d9d9c4ea5ec |
| ENCFF850NAU.tabix.bed.gz | 109.43 KB | f78c404bff796111e97368df92d5a846 |
| ENCFF850NAU.tabix.bed.gz.tbi | 87.0 KB | 7e7d331d8501a1501b4b7bdc040846cb |
| genomic_resource.yaml | 3.7 KB | 8b40b6be9e514f934706fcda5546366d |
| statistics/ |