Resource
| Id | Histone_ChIP-seq/ENCSR479BPF |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR479BPF [biosample_summary="Homo sapiens brain tissue female embryo (120 days)" and target="H3K27me3"] |
| Description |
status: released biological_replicates: Rep 1 summary: female embryo (120 days) output_type: pseudoreplicated peaks audit_internal_action: Archived analysis {ENCAN168TVN|/analyses/ENCAN168TVN/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF684CAP|/files/ENCFF684CAP/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 19419471 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 {ENCFF684CAP|/files/ENCFF684CAP/} processed by ChIP-seq ENCODE3 GRCh38 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 alignments file {ENCFF684CAP|/files/ENCFF684CAP/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 5.52. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR479BPF | float |
Histone_ChIP-seq_ENCSR479BPF |
Histone_ChIP-seq ENCSR479BPF [biosample_summary="Homo sapiens brain tissue female embryo (120 days)" and target="H3K27me3"]
|
 |
[2, 58.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 56948831 | 1.77% | 62313 |
| chr1 | 4781083 | 1.92% | 4972 |
| chr1_KI270713v1_random | 3934 | 9.66% | 4 |
| chr2 | 3388969 | 1.40% | 3541 |
| chr3 | 2078881 | 1.05% | 2500 |
| chr4 | 1938426 | 1.02% | 2008 |
| chr5 | 3344759 | 1.84% | 3383 |
| chr6 | 3153685 | 1.85% | 3222 |
| chr7 | 2395131 | 1.50% | 2399 |
| chr8 | 1875047 | 1.29% | 1897 |
| chr9 | 2162781 | 1.56% | 2185 |
| chr10 | 3453104 | 2.58% | 3609 |
| chr11 | 2504466 | 1.85% | 2632 |
| chr12 | 3104508 | 2.33% | 3337 |
| chr13 | 1082325 | 0.95% | 1175 |
| chr14 | 1807049 | 1.69% | 1870 |
| chr15 | 1832069 | 1.80% | 1934 |
| chr16 | 2823311 | 3.13% | 3114 |
| chr17 | 3387971 | 4.07% | 3240 |
| chr17_GL000205v2_random | 2517 | 1.36% | 1 |
| chr18 | 1128541 | 1.40% | 1349 |
| chr19 | 3010149 | 5.14% | 2998 |
| chr20 | 2563652 | 3.98% | 2936 |
| chr21 | 587739 | 1.26% | 625 |
| chr22 | 873494 | 1.72% | 988 |
| chr22_KI270733v1_random | 973 | 0.54% | 2 |
| chrX | 3664267 | 2.35% | 6392 |
| 3340 contigs with no values (185898392 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 62313 | 230 | 48765 | 913.92 | 546 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF591RMN.bed.gz | 1.16 MB | 3e34804b4e6ebde06c85c0e9a8d818b2 |
| ENCFF591RMN.tabix.bed.gz | 609.35 KB | 4399d615a4217aee0b6063e77c6b428a |
| ENCFF591RMN.tabix.bed.gz.tbi | 165.67 KB | 799e8130c61197617e0717183da45792 |
| genomic_resource.yaml | 3.24 KB | c2ae66b81cc817310362c09316482bc6 |
| statistics/ |