Resource
| Id | Histone_ChIP-seq/ENCSR000AQY |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000AQY [biosample_summary="Homo sapiens DND-41" and target="H3K4me1"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN024AJY|/analyses/ENCAN024AJY/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_internal_action: Released analysis {ENCAN024AJY|/analyses/ENCAN024AJY/} has in progress subobject document {8c975f13-7289-4f49-8daf-e707f9807d18|/documents/8c975f13-7289-4f49-8daf-e707f9807d18/} audit_not_compliant: Processed alignments file {ENCFF065CQJ|/files/ENCFF065CQJ/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 22893582 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 {ENCFF192WKN|/files/ENCFF192WKN/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 17960936 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 {ENCFF065CQJ|/files/ENCFF065CQJ/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.89. 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 {ENCFF065CQJ|/files/ENCFF065CQJ/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC2 value of 9.05. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000AQY | float |
Histone_ChIP-seq_ENCSR000AQY |
Histone_ChIP-seq ENCSR000AQY [biosample_summary="Homo sapiens DND-41" and target="H3K4me1"]
|
 |
[1.67, 71.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 100719334 | 3.13% | 77485 |
| chr1 | 9754052 | 3.92% | 7378 |
| chr2 | 8269968 | 3.41% | 6235 |
| chr3 | 6880213 | 3.47% | 5159 |
| chr4 | 4166274 | 2.19% | 3327 |
| chr5 | 5762984 | 3.17% | 4328 |
| chr6 | 5914911 | 3.46% | 4483 |
| chr7 | 4969675 | 3.12% | 3821 |
| chr8 | 3917934 | 2.70% | 3009 |
| chr9 | 3391568 | 2.45% | 2805 |
| chr10 | 4526505 | 3.38% | 3397 |
| chr11 | 4719519 | 3.49% | 3586 |
| chr12 | 4857452 | 3.64% | 3824 |
| chr13 | 2722533 | 2.38% | 1997 |
| chr14 | 3890684 | 3.63% | 2819 |
| chr15 | 2969648 | 2.91% | 2416 |
| chr16 | 3388686 | 3.75% | 2523 |
| chr17 | 4880454 | 5.86% | 3635 |
| chr18 | 2064921 | 2.57% | 1578 |
| chr19 | 3883156 | 6.62% | 3373 |
| chr20 | 2722368 | 4.22% | 2028 |
| chr21 | 1538609 | 3.29% | 1116 |
| chr22 | 2122430 | 4.18% | 1637 |
| chrX | 3069663 | 1.97% | 2717 |
| chrY | 335127 | 0.59% | 294 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 77485 | 168 | 40136 | 1299.86 | 898 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF035USI.bed.gz | 1.98 MB | 555ec00bf733d3349013e7a37f38c248 |
| ENCFF035USI.tabix.bed.gz | 859.17 KB | e3d35897d34b9555a9efdc9b9332e3be |
| ENCFF035USI.tabix.bed.gz.tbi | 233.27 KB | 220f1097cbd7d31dab53ca012c21309d |
| genomic_resource.yaml | 3.93 KB | 3ca2418b755b80e34a2ea335746296bd |
| statistics/ |