Resource
| Id | Histone_ChIP-seq/ENCSR628CTX |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR628CTX [biosample_summary="Homo sapiens muscle layer of duodenum tissue male adult (59 years)" and target="H3K4me1"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (59 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN385BWO|/analyses/ENCAN385BWO/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_not_compliant: Processed redacted alignments file {ENCFF587QOH|/files/ENCFF587QOH/} processed by ChIP-seq ENCODE4 v1.7.0 GRCh38 pipeline has 29925865 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 redacted alignments file {ENCFF587QOH|/files/ENCFF587QOH/} processed by ChIP-seq ENCODE4 v1.7.0 GRCh38 pipeline was generated from a library with PBC1 value of 0.86. 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 redacted alignments file {ENCFF587QOH|/files/ENCFF587QOH/} processed by ChIP-seq ENCODE4 v1.7.0 GRCh38 pipeline was generated from a library with PBC2 value of 7.02. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR628CTX | float |
Histone_ChIP-seq_ENCSR628CTX |
Histone_ChIP-seq ENCSR628CTX [biosample_summary="Homo sapiens muscle layer of duodenum tissue male adult (59 years)" and target="H3K4me1"]
|
 |
[1.66, 9.73] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 24677539 | 0.77% | 37798 |
| chr1 | 2818501 | 1.13% | 4171 |
| chr2 | 1916516 | 0.79% | 2981 |
| chr3 | 1701246 | 0.86% | 2613 |
| chr4 | 900017 | 0.47% | 1439 |
| chr5 | 1280506 | 0.71% | 1917 |
| chr6 | 1329911 | 0.78% | 2107 |
| chr7 | 965395 | 0.61% | 1575 |
| chr8 | 893035 | 0.62% | 1401 |
| chr9 | 1169115 | 0.84% | 1794 |
| chr10 | 1377129 | 1.03% | 2042 |
| chr11 | 1492403 | 1.10% | 2270 |
| chr12 | 1316890 | 0.99% | 1963 |
| chr13 | 507670 | 0.44% | 795 |
| chr14 | 945309 | 0.88% | 1379 |
| chr15 | 939248 | 0.92% | 1399 |
| chr16 | 788395 | 0.87% | 1238 |
| chr17 | 1408368 | 1.69% | 2089 |
| chr18 | 401382 | 0.50% | 647 |
| chr19 | 778005 | 1.33% | 1238 |
| chr20 | 734750 | 1.14% | 1084 |
| chr21 | 228137 | 0.49% | 371 |
| chr22 | 625599 | 1.23% | 955 |
| chrX | 158425 | 0.10% | 326 |
| chrY | 1587 | <0.01% | 4 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 37798 | 225 | 6297 | 652.88 | 556 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF395OSQ.bed.gz | 752.8 KB | 80bb30f5d2ae13478976181355224314 |
| ENCFF395OSQ.tabix.bed.gz | 383.59 KB | 5eee56d41ba03e9d886ab0dfdac84b15 |
| ENCFF395OSQ.tabix.bed.gz.tbi | 175.38 KB | 8f7371125a1e0ceeeb7a297b5825e9be |
| genomic_resource.yaml | 3.33 KB | 2a2c593140cad4148b39e94caba55e38 |
| statistics/ |