Resource
| Id | Histone_ChIP-seq/ENCSR023ALV |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR023ALV [biosample_summary="Homo sapiens heart right ventricle tissue male child (3 years)" and target="H3K4me1"] |
| Description |
status: released biological_replicates: Rep 1 summary: male child (3 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN707XEL|/analyses/ENCAN707XEL/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_internal_action: Released analysis {ENCAN707XEL|/analyses/ENCAN707XEL/} has in progress subobject document {a1e4545f-e204-4505-86a5-aa0f784b8140|/documents/a1e4545f-e204-4505-86a5-aa0f784b8140/} audit_not_compliant: Processed alignments file {ENCFF338PND|/files/ENCFF338PND/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 13531418 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 {ENCFF338PND|/files/ENCFF338PND/} 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 {ENCFF338PND|/files/ENCFF338PND/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 9.41. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR023ALV | float |
Histone_ChIP-seq_ENCSR023ALV |
Histone_ChIP-seq ENCSR023ALV [biosample_summary="Homo sapiens heart right ventricle tissue male child (3 years)" and target="H3K4me1"]
|
 |
[2.01, 9.7] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 14534288 | 0.45% | 45729 |
| chr1 | 1441357 | 0.58% | 4487 |
| chr2 | 1297015 | 0.54% | 4107 |
| chr3 | 1285175 | 0.65% | 4049 |
| chr4 | 816529 | 0.43% | 2706 |
| chr5 | 1018811 | 0.56% | 3234 |
| chr6 | 932148 | 0.55% | 2995 |
| chr7 | 728273 | 0.46% | 2364 |
| chr8 | 687630 | 0.47% | 2160 |
| chr9 | 599345 | 0.43% | 1874 |
| chr10 | 816396 | 0.61% | 2519 |
| chr11 | 706247 | 0.52% | 2175 |
| chr12 | 716565 | 0.54% | 2281 |
| chr13 | 415709 | 0.36% | 1367 |
| chr14 | 466932 | 0.44% | 1420 |
| chr15 | 535088 | 0.52% | 1656 |
| chr16 | 295143 | 0.33% | 904 |
| chr17 | 422954 | 0.51% | 1268 |
| chr18 | 324031 | 0.40% | 1063 |
| chr19 | 214439 | 0.37% | 589 |
| chr20 | 320789 | 0.50% | 915 |
| chr21 | 120894 | 0.26% | 382 |
| chr22 | 229703 | 0.45% | 655 |
| chrX | 139743 | 0.09% | 544 |
| chrY | 3372 | 0.01% | 15 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 45729 | 150 | 2173 | 317.84 | 277 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF072QWS.bed.gz | 820.81 KB | 7a31293015e3d561e77ab5a8ef792c29 |
| ENCFF072QWS.tabix.bed.gz | 423.89 KB | 2d3b2e8c174b4def369458b8c6f9b824 |
| ENCFF072QWS.tabix.bed.gz.tbi | 201.03 KB | 5d452feb980d064c3d479dad7fe3012a |
| genomic_resource.yaml | 3.49 KB | cffbb1e0a0df42e612891be7ed5a4173 |
| statistics/ |