Resource
| Id | Histone_ChIP-seq/ENCSR292WQY |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR292WQY [biosample_summary="Homo sapiens endocrine pancreas tissue male adult (46 years)" and target="H3K4me1"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (46 years) output_type: pseudoreplicated peaks audit_internal_action: Archived analysis {ENCAN778VBP|/analyses/ENCAN778VBP/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed redacted alignments file {ENCFF763DXP|/files/ENCFF763DXP/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 5335469 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 {ENCFF763DXP|/files/ENCFF763DXP/} processed by ChIP-seq ENCODE3 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 redacted alignments file {ENCFF763DXP|/files/ENCFF763DXP/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 9.58. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR292WQY | float |
Histone_ChIP-seq_ENCSR292WQY |
Histone_ChIP-seq ENCSR292WQY [biosample_summary="Homo sapiens endocrine pancreas tissue male adult (46 years)" and target="H3K4me1"]
|
 |
[2.16, 16.3] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 34369877 | 1.07% | 52534 |
| chr1 | 3085139 | 1.24% | 4642 |
| chr2 | 2973007 | 1.23% | 4559 |
| chr3 | 2878678 | 1.45% | 4399 |
| chr4 | 2391381 | 1.26% | 3658 |
| chr5 | 2478168 | 1.37% | 3699 |
| chr6 | 2501621 | 1.46% | 3794 |
| chr7 | 2079377 | 1.30% | 3192 |
| chr8 | 1797398 | 1.24% | 2717 |
| chr9 | 1351854 | 0.98% | 2069 |
| chr10 | 1651543 | 1.23% | 2514 |
| chr11 | 1547230 | 1.15% | 2360 |
| chr12 | 1673743 | 1.26% | 2571 |
| chr13 | 1351375 | 1.18% | 2073 |
| chr14 | 1156145 | 1.08% | 1786 |
| chr15 | 1105626 | 1.08% | 1612 |
| chr16 | 607041 | 0.67% | 952 |
| chr17 | 930092 | 1.12% | 1427 |
| chr18 | 839735 | 1.04% | 1313 |
| chr19 | 178679 | 0.30% | 313 |
| chr20 | 722190 | 1.12% | 1077 |
| chr21 | 327112 | 0.70% | 518 |
| chr22 | 316729 | 0.62% | 476 |
| chrUn_KI270467v1 | 1672 | 42.65% | 1 |
| chrX | 412412 | 0.26% | 790 |
| chrY | 11930 | 0.02% | 22 |
| 3341 contigs with no values (129073165 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 52534 | 270 | 5781 | 654.24 | 564 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF571ZWG.bed.gz | 977.29 KB | 9ca49d8040093cca1b8f3781bcbc99af |
| ENCFF571ZWG.tabix.bed.gz | 510.07 KB | a4515b7e70d7d065140d3e077b075266 |
| ENCFF571ZWG.tabix.bed.gz.tbi | 224.29 KB | dca98d59336d93c03b635745f1846f0d |
| genomic_resource.yaml | 3.28 KB | 7b3c9a9643a63a0d1cbde3da04ce4cab |
| statistics/ |