Resource
| Id | Histone_ChIP-seq/ENCSR268BMX |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR268BMX [biosample_summary="Homo sapiens foreskin keratinocyte male newborn" and target="H3K27me3"] |
| Description |
status: released biological_replicates: Rep 1 summary: male newborn output_type: pseudoreplicated peaks audit_internal_action: Archived analysis {ENCAN658TGL|/analyses/ENCAN658TGL/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed redacted alignments file {ENCFF293NKP|/files/ENCFF293NKP/} processed by ChIP-seq ENCODE3 hg19 pipeline has 32342054 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K27me3-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 {ENCFF293NKP|/files/ENCFF293NKP/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.82. 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 {ENCFF293NKP|/files/ENCFF293NKP/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 5.58. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR268BMX | float |
Histone_ChIP-seq_ENCSR268BMX |
Histone_ChIP-seq ENCSR268BMX [biosample_summary="Homo sapiens foreskin keratinocyte male newborn" and target="H3K27me3"]
|
 |
[1.6, 26] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 45126002 | 1.40% | 80019 |
| chr1 | 4185038 | 1.68% | 7596 |
| chr2 | 3205534 | 1.32% | 5819 |
| chr3 | 2020662 | 1.02% | 3904 |
| chr4 | 1823222 | 0.96% | 3137 |
| chr5 | 2165052 | 1.19% | 3927 |
| chr6 | 2115796 | 1.24% | 3803 |
| chr7 | 2398368 | 1.51% | 4179 |
| chr8 | 1851895 | 1.28% | 3452 |
| chr9 | 2151306 | 1.55% | 3594 |
| chr10 | 2473068 | 1.85% | 4377 |
| chr11 | 2666544 | 1.97% | 4759 |
| chr12 | 1924800 | 1.44% | 3515 |
| chr13 | 1121047 | 0.98% | 1982 |
| chr14 | 1518615 | 1.42% | 2677 |
| chr15 | 1516683 | 1.49% | 2834 |
| chr16 | 1917582 | 2.12% | 3331 |
| chr17 | 2984381 | 3.58% | 4790 |
| chr18 | 781865 | 0.97% | 1523 |
| chr19 | 2026785 | 3.46% | 3211 |
| chr20 | 2207468 | 3.43% | 3920 |
| chr21 | 506671 | 1.08% | 944 |
| chr22 | 1119531 | 2.20% | 2123 |
| chrX | 441393 | 0.28% | 616 |
| chrY | 2696 | <0.01% | 6 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 80019 | 170 | 27261 | 563.94 | 335 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF751NUT.bed.gz | 1.47 MB | b6b140106deedf3f3389a816e84695f8 |
| ENCFF751NUT.tabix.bed.gz | 777.56 KB | 7d49ebbb36d3f8aa33bf74fbd3fe71b3 |
| ENCFF751NUT.tabix.bed.gz.tbi | 228.05 KB | bf7652b19f9c6501caa625ffebad8a7b |
| genomic_resource.yaml | 3.23 KB | 7df202b28f8c1525669f4f370d3e4214 |
| statistics/ |