Resource
| Id | Histone_ChIP-seq/ENCSR000AMS |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000AMS [biosample_summary="Homo sapiens fibroblast of lung female child (11 years) and male adult (45 years)" and target="H3K27me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: female child (11 years) male adult (45 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN563ZZP|/analyses/ENCAN563ZZP/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_internal_action: Released analysis {ENCAN563ZZP|/analyses/ENCAN563ZZP/} has in progress subobject document {a8d7b97d-2770-4fad-bf53-3fa8065b4cd2|/documents/a8d7b97d-2770-4fad-bf53-3fa8065b4cd2/} audit_not_compliant: Processed alignments file {ENCFF316JBQ|/files/ENCFF316JBQ/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 6697413 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_not_compliant: Processed alignments file {ENCFF536KWZ|/files/ENCFF536KWZ/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 7893229 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 alignments file {ENCFF316JBQ|/files/ENCFF316JBQ/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.90. 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 {ENCFF316JBQ|/files/ENCFF316JBQ/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC2 value of 9.76. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000AMS | float |
Histone_ChIP-seq_ENCSR000AMS |
Histone_ChIP-seq ENCSR000AMS [biosample_summary="Homo sapiens fibroblast of lung female child (11 years) and male adult (45 years)" and target="H3K27me3"]
|
 |
[1.93, 17.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 22103015 | 0.69% | 44385 |
| chr1 | 2566294 | 1.03% | 5075 |
| chr2 | 1936086 | 0.80% | 3872 |
| chr3 | 1185798 | 0.60% | 2524 |
| chr4 | 679179 | 0.36% | 1351 |
| chr5 | 1042195 | 0.57% | 2142 |
| chr6 | 1124345 | 0.66% | 2184 |
| chr7 | 963391 | 0.60% | 1868 |
| chr8 | 876625 | 0.60% | 1904 |
| chr9 | 1066309 | 0.77% | 2131 |
| chr10 | 1240784 | 0.93% | 2510 |
| chr11 | 1372839 | 1.02% | 2963 |
| chr12 | 963037 | 0.72% | 1818 |
| chr13 | 519080 | 0.45% | 1028 |
| chr14 | 655003 | 0.61% | 1290 |
| chr15 | 945079 | 0.93% | 1973 |
| chr16 | 623699 | 0.69% | 1301 |
| chr17 | 1473774 | 1.77% | 2686 |
| chr18 | 346679 | 0.43% | 766 |
| chr19 | 674068 | 1.15% | 1210 |
| chr20 | 899807 | 1.40% | 1769 |
| chr21 | 250979 | 0.54% | 507 |
| chr22 | 542185 | 1.07% | 1156 |
| chrX | 155780 | 0.10% | 357 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 44385 | 173 | 13288 | 497.98 | 365 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF718BNY.bed.gz | 758.2 KB | ab18fa87dcc6beea699777d55c84854b |
| ENCFF718BNY.tabix.bed.gz | 408.21 KB | 47c32cf8af11b59178a1cab31a3ad44e |
| ENCFF718BNY.tabix.bed.gz.tbi | 135.47 KB | 8a2902e93f454e47ef36714965954fc9 |
| genomic_resource.yaml | 4.1 KB | aa79d57d1dffdd9447d8f13aa97c6c89 |
| statistics/ |