Resource
| Id | Histone_ChIP-seq/ENCSR000EXV |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000EXV [biosample_summary="Homo sapiens mononuclear cell male" and target="H3K4me1"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: male output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN388ZFW|/analyses/ENCAN388ZFW/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_internal_action: Released analysis {ENCAN388ZFW|/analyses/ENCAN388ZFW/} has in progress subobject document {31cff06a-e7aa-402f-b8f1-d2cc97c36d4b|/documents/31cff06a-e7aa-402f-b8f1-d2cc97c36d4b/} audit_not_compliant: Processed alignments file {ENCFF424AKL|/files/ENCFF424AKL/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 14768617 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me1-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 {ENCFF305NHF|/files/ENCFF305NHF/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 30079072 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me1-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 {ENCFF305NHF|/files/ENCFF305NHF/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.88. 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 {ENCFF305NHF|/files/ENCFF305NHF/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC2 value of 8.25. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000EXV | float |
Histone_ChIP-seq_ENCSR000EXV |
Histone_ChIP-seq ENCSR000EXV [biosample_summary="Homo sapiens mononuclear cell male" and target="H3K4me1"]
|
 |
[1.64, 31.2] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 146998735 | 4.57% | 128557 |
| chr1 | 14540438 | 5.84% | 12533 |
| chr2 | 11794033 | 4.87% | 10678 |
| chr3 | 9149893 | 4.61% | 8597 |
| chr4 | 5171667 | 2.72% | 5238 |
| chr5 | 7169442 | 3.95% | 6635 |
| chr6 | 8836337 | 5.17% | 8230 |
| chr7 | 6515252 | 4.09% | 6154 |
| chr8 | 5874049 | 4.05% | 5383 |
| chr9 | 6122410 | 4.42% | 5251 |
| chr10 | 7070593 | 5.28% | 6160 |
| chr11 | 7661722 | 5.67% | 6199 |
| chr12 | 7777777 | 5.84% | 6914 |
| chr13 | 2974439 | 2.60% | 2996 |
| chr14 | 5170308 | 4.83% | 4351 |
| chr15 | 5180903 | 5.08% | 4266 |
| chr16 | 5700387 | 6.31% | 4386 |
| chr17 | 8272740 | 9.94% | 6346 |
| chr18 | 2608936 | 3.25% | 2400 |
| chr19 | 6560816 | 11.19% | 4966 |
| chr20 | 4633523 | 7.19% | 3684 |
| chr21 | 1775738 | 3.80% | 1519 |
| chr22 | 3458569 | 6.81% | 2638 |
| chrX | 2865987 | 1.84% | 2897 |
| chrY | 112776 | 0.20% | 136 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 128557 | 230 | 33482 | 1143.45 | 789 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF767YTL.bed.gz | 2.96 MB | 047e3804acfba23e75be227c37b97501 |
| ENCFF767YTL.tabix.bed.gz | 1.32 MB | c559b54644546670fcbddc174afd6b89 |
| ENCFF767YTL.tabix.bed.gz.tbi | 273.22 KB | 0a1f5a52dc0975f8e6c4f5da7061a51a |
| genomic_resource.yaml | 3.87 KB | 5ac829c94a284160d3974d86c2d137d2 |
| statistics/ |