Resource
| Id | Histone_ChIP-seq/ENCSR000AQT |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000AQT [biosample_summary="Homo sapiens osteoblast" and target="H4K20me1"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN932KLY|/analyses/ENCAN932KLY/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF769AQO|/files/ENCFF769AQO/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 8474307 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_not_compliant: Processed alignments file {ENCFF540VPY|/files/ENCFF540VPY/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 24334848 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 {ENCFF540VPY|/files/ENCFF540VPY/} 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 alignments file {ENCFF540VPY|/files/ENCFF540VPY/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 8.99. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000AQT | float |
Histone_ChIP-seq_ENCSR000AQT |
Histone_ChIP-seq ENCSR000AQT [biosample_summary="Homo sapiens osteoblast" and target="H4K20me1"]
|
 |
[1.75, 18.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 60403012 | 1.88% | 98967 |
| chr1 | 5603087 | 2.25% | 9114 |
| chr2 | 4557431 | 1.88% | 7483 |
| chr3 | 3997802 | 2.02% | 6652 |
| chr4 | 2003904 | 1.05% | 3523 |
| chr5 | 3162456 | 1.74% | 5120 |
| chr6 | 2422019 | 1.42% | 4124 |
| chr7 | 3173745 | 1.99% | 5364 |
| chr8 | 2276653 | 1.57% | 3740 |
| chr9 | 2841528 | 2.05% | 4480 |
| chr10 | 3231503 | 2.42% | 5510 |
| chr11 | 3334674 | 2.47% | 5383 |
| chr12 | 2781368 | 2.09% | 4738 |
| chr13 | 1295427 | 1.13% | 2250 |
| chr14 | 1972373 | 1.84% | 3340 |
| chr15 | 2254852 | 2.21% | 3875 |
| chr16 | 2934199 | 3.25% | 4482 |
| chr17 | 3524011 | 4.23% | 5503 |
| chr18 | 994536 | 1.24% | 1671 |
| chr19 | 2733929 | 4.66% | 4072 |
| chr20 | 1951669 | 3.03% | 2945 |
| chr21 | 612398 | 1.31% | 1029 |
| chr22 | 1875190 | 3.69% | 2900 |
| chrX | 868258 | 0.56% | 1669 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 98967 | 165 | 17296 | 610.33 | 449 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF938HJZ.bed.gz | 1.98 MB | ff94126c25b3bbca652c5d714d9e1ac0 |
| ENCFF938HJZ.tabix.bed.gz | 977.28 KB | 795a796556cfce26bfa0a9124d264eeb |
| ENCFF938HJZ.tabix.bed.gz.tbi | 158.48 KB | 19b21a837003cc113eb7db1bf6a2049e |
| genomic_resource.yaml | 3.69 KB | 9653466e92cfc753e944e5dc7dccc42d |
| statistics/ |