Resource
| Id | Histone_ChIP-seq/ENCSR416CYZ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR416CYZ [biosample_summary="Homo sapiens thoracic aorta tissue male adult (54 years)" and target="H3K4me1"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: male adult (54 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN843MVE|/analyses/ENCAN843MVE/} has in progress subobject document {319d4a36-b544-4839-ae20-8885486a579d|/documents/319d4a36-b544-4839-ae20-8885486a579d/} audit_internal_action: Released analysis {ENCAN843MVE|/analyses/ENCAN843MVE/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_warning: Processed alignments file {ENCFF756ZJP|/files/ENCFF756ZJP/} processed by ChIP-seq ENCODE4 v1.6.0 GRCh38 pipeline has 44043653 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 {ENCFF542KRW|/files/ENCFF542KRW/} processed by ChIP-seq ENCODE4 v1.6.0 GRCh38 pipeline was generated from a library with PBC1 value of 0.85. 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 {ENCFF542KRW|/files/ENCFF542KRW/} processed by ChIP-seq ENCODE4 v1.6.0 GRCh38 pipeline was generated from a library with PBC2 value of 6.38. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR416CYZ | float |
Histone_ChIP-seq_ENCSR416CYZ |
Histone_ChIP-seq ENCSR416CYZ [biosample_summary="Homo sapiens thoracic aorta tissue male adult (54 years)" and target="H3K4me1"]
|
 |
[1.61, 7.18] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 72942003 | 2.27% | 108215 |
| chr1 | 7141386 | 2.87% | 10319 |
| chr2 | 6339305 | 2.62% | 9414 |
| chr3 | 5891736 | 2.97% | 8735 |
| chr4 | 3501737 | 1.84% | 5556 |
| chr5 | 4107205 | 2.26% | 6275 |
| chr6 | 4267515 | 2.50% | 6636 |
| chr7 | 3384806 | 2.12% | 5221 |
| chr8 | 3096452 | 2.13% | 4759 |
| chr9 | 3276409 | 2.37% | 4766 |
| chr10 | 4388063 | 3.28% | 6402 |
| chr11 | 3755636 | 2.78% | 5305 |
| chr12 | 3909556 | 2.93% | 5729 |
| chr13 | 1709545 | 1.49% | 2689 |
| chr14 | 2307584 | 2.16% | 3348 |
| chr15 | 2692633 | 2.64% | 3872 |
| chr16 | 2203132 | 2.44% | 3261 |
| chr17 | 3151467 | 3.79% | 4445 |
| chr18 | 1346836 | 1.68% | 2058 |
| chr19 | 2032212 | 3.47% | 2865 |
| chr20 | 1862359 | 2.89% | 2672 |
| chr21 | 816472 | 1.75% | 1243 |
| chr22 | 1374927 | 2.71% | 1902 |
| chrX | 382486 | 0.25% | 736 |
| chrY | 2544 | <0.01% | 7 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 108215 | 223 | 10785 | 674.05 | 532 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF887LPK.bed.gz | 2.32 MB | 44f8371e2ce68ba709ee395ccf401f91 |
| ENCFF887LPK.tabix.bed.gz | 1.11 MB | 049caaf5fb69f512a8e0fc71470f23a7 |
| ENCFF887LPK.tabix.bed.gz.tbi | 304.21 KB | 502b8eff8fb388058ac76f8d2aa6a5ca |
| genomic_resource.yaml | 3.47 KB | 63f1713c16c53b1b29f8035de4c473f6 |
| statistics/ |