Resource
| Id | Histone_ChIP-seq/ENCSR000ARJ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000ARJ [biosample_summary="Homo sapiens fibroblast of dermis" and target="H4K20me1"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2, Rep 3 summary: output_type: pseudoreplicated peaks audit_error: Processed alignments file {ENCFF625YGE|/files/ENCFF625YGE/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 3651053 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_error: Processed alignments file {ENCFF934EYV|/files/ENCFF934EYV/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 4999806 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_internal_action: Released analysis {ENCAN724MIC|/analyses/ENCAN724MIC/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_internal_action: Released analysis {ENCAN724MIC|/analyses/ENCAN724MIC/} has in progress subobject document {c00bb442-0d3e-46e8-8956-0bb4a0df8998|/documents/c00bb442-0d3e-46e8-8956-0bb4a0df8998/} audit_not_compliant: Processed alignments file {ENCFF290BBE|/files/ENCFF290BBE/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 7667563 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 {ENCFF625YGE|/files/ENCFF625YGE/} 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 {ENCFF625YGE|/files/ENCFF625YGE/} processed by ChIP-seq ENCODE4 v1.6.1 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_ENCSR000ARJ | float |
Histone_ChIP-seq_ENCSR000ARJ |
Histone_ChIP-seq ENCSR000ARJ [biosample_summary="Homo sapiens fibroblast of dermis" and target="H4K20me1"]
|
 |
[2.03, 15.2] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 21040221 | 0.65% | 25016 |
| chr1 | 1870360 | 0.75% | 2085 |
| chr2 | 1628621 | 0.67% | 1933 |
| chr3 | 1185913 | 0.60% | 1491 |
| chr4 | 507850 | 0.27% | 692 |
| chr5 | 1099568 | 0.61% | 1309 |
| chr6 | 708254 | 0.41% | 879 |
| chr7 | 906094 | 0.57% | 1216 |
| chr8 | 869977 | 0.60% | 1014 |
| chr9 | 1010058 | 0.73% | 1151 |
| chr10 | 1105884 | 0.83% | 1409 |
| chr11 | 1256077 | 0.93% | 1416 |
| chr12 | 1010844 | 0.76% | 1196 |
| chr13 | 330659 | 0.29% | 452 |
| chr14 | 609275 | 0.57% | 764 |
| chr15 | 726258 | 0.71% | 890 |
| chr16 | 1112940 | 1.23% | 1284 |
| chr17 | 1452888 | 1.75% | 1560 |
| chr18 | 455451 | 0.57% | 480 |
| chr19 | 1271750 | 2.17% | 1436 |
| chr20 | 651938 | 1.01% | 825 |
| chr21 | 245825 | 0.53% | 281 |
| chr22 | 723065 | 1.42% | 855 |
| chrX | 300672 | 0.19% | 398 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 25016 | 248 | 17428 | 841.07 | 639 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF949HTC.bed.gz | 544.03 KB | 6bdf5ee725d6a4e791d341499bd389d3 |
| ENCFF949HTC.tabix.bed.gz | 261.8 KB | 3453c67bad1182e1ca6b39f9e201dd56 |
| ENCFF949HTC.tabix.bed.gz.tbi | 82.35 KB | b5a3f455749add3cc6f7f04259c1e9e4 |
| genomic_resource.yaml | 4.47 KB | aa73fb9000f6bf5ecc2d818643bff7b3 |
| statistics/ |