Resource
| Id | Histone_ChIP-seq/ENCSR960ZMM |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR960ZMM [biosample_summary="Homo sapiens OCI-LY1" and target="H4K20me1"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN902AXY|/analyses/ENCAN902AXY/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF729YBU|/files/ENCFF729YBU/} processed by ChIP-seq ENCODE3 hg19 pipeline has 25188316 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H4K20me1-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 {ENCFF454HDW|/files/ENCFF454HDW/} processed by ChIP-seq ENCODE3 hg19 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 {ENCFF454HDW|/files/ENCFF454HDW/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 7.65. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR960ZMM | float |
Histone_ChIP-seq_ENCSR960ZMM |
Histone_ChIP-seq ENCSR960ZMM [biosample_summary="Homo sapiens OCI-LY1" and target="H4K20me1"]
|
 |
[1.56, 4.53] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 1249333 | 0.04% | 3813 |
| chr1 | 112585 | 0.05% | 338 |
| chr2 | 96001 | 0.04% | 298 |
| chr3 | 135029 | 0.07% | 383 |
| chr4 | 50891 | 0.03% | 154 |
| chr5 | 69178 | 0.04% | 219 |
| chr6 | 69227 | 0.04% | 222 |
| chr7 | 145412 | 0.09% | 444 |
| chr8 | 92652 | 0.06% | 279 |
| chr9 | 37176 | 0.03% | 118 |
| chr10 | 48762 | 0.04% | 150 |
| chr11 | 36600 | 0.03% | 116 |
| chr12 | 54675 | 0.04% | 163 |
| chr13 | 59228 | 0.05% | 183 |
| chr14 | 35000 | 0.03% | 105 |
| chr15 | 23871 | 0.02% | 79 |
| chr16 | 37279 | 0.04% | 119 |
| chr17 | 37886 | 0.05% | 119 |
| chr18 | 23319 | 0.03% | 72 |
| chr19 | 21863 | 0.04% | 69 |
| chr20 | 35530 | 0.06% | 99 |
| chr21 | 10564 | 0.02% | 34 |
| chr22 | 14634 | 0.03% | 43 |
| chrX | 1699 | <0.01% | 6 |
| chrY | 272 | <0.01% | 1 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 3813 | 195 | 2266 | 327.65 | 282 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF521WMG.bed.gz | 78.63 KB | cdfbc158f7e7a2173f669b69c391bdb8 |
| ENCFF521WMG.tabix.bed.gz | 40.74 KB | b0a2e348dfa9532326f54b6cd672f26d |
| ENCFF521WMG.tabix.bed.gz.tbi | 31.18 KB | 9f555d1dd9e65eb74d167a6c859dbe59 |
| genomic_resource.yaml | 3.17 KB | b5abcd261995dbfa5d252ebba4fa3a0d |
| statistics/ |