Resource
| Id | Histone_ChIP-seq/ENCSR790QWJ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR790QWJ [biosample_summary="Homo sapiens KMS-11" and target="H4K20me1"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN291UQF|/analyses/ENCAN291UQF/} has in progress subobject document {ab4a78a8-8de2-408d-8411-c7e44d01904d|/documents/ab4a78a8-8de2-408d-8411-c7e44d01904d/} audit_internal_action: Released analysis {ENCAN291UQF|/analyses/ENCAN291UQF/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF123YHG|/files/ENCFF123YHG/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 24268161 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H4K20me1-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 {ENCFF901QZZ|/files/ENCFF901QZZ/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 14232565 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H4K20me1-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 {ENCFF901QZZ|/files/ENCFF901QZZ/} processed by ChIP-seq ENCODE4 v1.6.1 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 {ENCFF901QZZ|/files/ENCFF901QZZ/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 7.39. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR790QWJ | float |
Histone_ChIP-seq_ENCSR790QWJ |
Histone_ChIP-seq ENCSR790QWJ [biosample_summary="Homo sapiens KMS-11" and target="H4K20me1"]
|
 |
[1.72, 9.51] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 10489773 | 0.33% | 11653 |
| chr1 | 1053298 | 0.42% | 1112 |
| chr2 | 839197 | 0.35% | 908 |
| chr3 | 786696 | 0.40% | 745 |
| chr4 | 416416 | 0.22% | 489 |
| chr5 | 623063 | 0.34% | 648 |
| chr6 | 509223 | 0.30% | 606 |
| chr7 | 922272 | 0.58% | 1022 |
| chr8 | 559885 | 0.39% | 590 |
| chr9 | 375435 | 0.27% | 439 |
| chr10 | 614845 | 0.46% | 730 |
| chr11 | 375884 | 0.28% | 449 |
| chr12 | 545036 | 0.41% | 582 |
| chr13 | 76392 | 0.07% | 101 |
| chr14 | 140105 | 0.13% | 168 |
| chr15 | 250586 | 0.25% | 349 |
| chr16 | 544681 | 0.60% | 562 |
| chr17 | 424025 | 0.51% | 512 |
| chr18 | 214513 | 0.27% | 267 |
| chr19 | 388116 | 0.66% | 420 |
| chr20 | 383833 | 0.60% | 426 |
| chr21 | 125425 | 0.27% | 142 |
| chr22 | 225512 | 0.44% | 268 |
| chrX | 95335 | 0.06% | 118 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 11653 | 203 | 16589 | 900.18 | 634 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF882SPY.bed.gz | 260.98 KB | 697cfbf96c67cd55890038b85285351f |
| ENCFF882SPY.tabix.bed.gz | 124.0 KB | 2f8685bfa4581d04e976d9a366ec68da |
| ENCFF882SPY.tabix.bed.gz.tbi | 44.68 KB | bf538eec46e8c9b5611775e2c832afbe |
| genomic_resource.yaml | 3.93 KB | ec4887738fe116d167b0691f53decc43 |
| statistics/ |