Resource
| Id | Histone_ChIP-seq/ENCSR293NAJ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR293NAJ [biosample_summary="Homo sapiens GM23338 originated from GM23248" and target="H4K20me1"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Released analysis {ENCAN390BIN|/analyses/ENCAN390BIN/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF254FGF|/files/ENCFF254FGF/} processed by ChIP-seq ENCODE4 v1.8.0 GRCh38 pipeline has 27499762 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 {ENCFF480HKL|/files/ENCFF480HKL/} processed by ChIP-seq ENCODE4 v1.8.0 GRCh38 pipeline has 16265007 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 {ENCFF480HKL|/files/ENCFF480HKL/} processed by ChIP-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with PBC1 value of 0.81. 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 {ENCFF480HKL|/files/ENCFF480HKL/} processed by ChIP-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with PBC2 value of 5.09. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR293NAJ | float |
Histone_ChIP-seq_ENCSR293NAJ |
Histone_ChIP-seq ENCSR293NAJ [biosample_summary="Homo sapiens GM23338 originated from GM23248" and target="H4K20me1"]
|
 |
[1.46, 10.1] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 51399333 | 1.60% | 66948 |
| chr1 | 5519958 | 2.22% | 7085 |
| chr2 | 4069995 | 1.68% | 5431 |
| chr3 | 2985945 | 1.51% | 3929 |
| chr4 | 1874845 | 0.99% | 2502 |
| chr5 | 2723462 | 1.50% | 3440 |
| chr6 | 2593942 | 1.52% | 3192 |
| chr7 | 2851455 | 1.79% | 3768 |
| chr8 | 2166412 | 1.49% | 2779 |
| chr9 | 2105028 | 1.52% | 3007 |
| chr10 | 2282605 | 1.71% | 2967 |
| chr11 | 2368208 | 1.75% | 3181 |
| chr12 | 2626728 | 1.97% | 3561 |
| chr13 | 1066901 | 0.93% | 1439 |
| chr14 | 1572321 | 1.47% | 2075 |
| chr15 | 1840325 | 1.80% | 2495 |
| chr16 | 2288643 | 2.53% | 2828 |
| chr17 | 2846044 | 3.42% | 3668 |
| chr18 | 679756 | 0.85% | 1022 |
| chr19 | 2455936 | 4.19% | 3005 |
| chr20 | 1829469 | 2.84% | 2143 |
| chr21 | 545011 | 1.17% | 730 |
| chr22 | 1747096 | 3.44% | 2137 |
| chrX | 346248 | 0.22% | 542 |
| chrY | 13000 | 0.02% | 22 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 66948 | 180 | 20304 | 767.75 | 567 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF300RQZ.bed.gz | 1.42 MB | 03d0e4b6c64266a011638aa2762b20d4 |
| ENCFF300RQZ.tabix.bed.gz | 679.12 KB | 8ea3c208f90340f8c7bbc7823187e388 |
| ENCFF300RQZ.tabix.bed.gz.tbi | 160.74 KB | 0e93d4ba137fd36702fdedc9484c144c |
| genomic_resource.yaml | 3.78 KB | 2fb4d5686988eed15bf023dbeb725700 |
| statistics/ |