Resource
| Id | Histone_ChIP-seq/ENCSR000FCG |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000FCG [biosample_summary="Homo sapiens HEK293" and target="H3K4me1"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN159UNJ|/analyses/ENCAN159UNJ/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF909ESY|/files/ENCFF909ESY/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 7514960 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me1-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 {ENCFF115NAM|/files/ENCFF115NAM/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 25033797 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me1-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 {ENCFF909ESY|/files/ENCFF909ESY/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.85. 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 {ENCFF909ESY|/files/ENCFF909ESY/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 6.67. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000FCG | float |
Histone_ChIP-seq_ENCSR000FCG |
Histone_ChIP-seq ENCSR000FCG [biosample_summary="Homo sapiens HEK293" and target="H3K4me1"]
|
 |
[1.77, 17.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 37377423 | 1.16% | 77523 |
| chr1 | 3246323 | 1.30% | 6650 |
| chr2 | 3301177 | 1.36% | 7037 |
| chr3 | 1262877 | 0.64% | 3117 |
| chr4 | 987221 | 0.52% | 2516 |
| chr5 | 3051143 | 1.68% | 5918 |
| chr6 | 3497413 | 2.05% | 6577 |
| chr7 | 2015025 | 1.26% | 4202 |
| chr8 | 749930 | 0.52% | 1953 |
| chr9 | 1058960 | 0.77% | 2576 |
| chr10 | 2372943 | 1.77% | 4835 |
| chr11 | 618926 | 0.46% | 1629 |
| chr12 | 2173088 | 1.63% | 4535 |
| chr13 | 517730 | 0.45% | 1347 |
| chr14 | 1734172 | 1.62% | 3497 |
| chr15 | 1855354 | 1.82% | 3477 |
| chr16 | 927130 | 1.03% | 2047 |
| chr17 | 2391787 | 2.87% | 4441 |
| chr18 | 1394816 | 1.74% | 2692 |
| chr19 | 1480092 | 2.52% | 2709 |
| chr20 | 826716 | 1.28% | 1804 |
| chr21 | 540567 | 1.16% | 997 |
| chr22 | 696583 | 1.37% | 1397 |
| chrUn_GL000195v1 | 1055 | 0.58% | 3 |
| chrUn_KI270438v1 | 342 | 0.30% | 1 |
| chrX | 676053 | 0.43% | 1566 |
| 3341 contigs with no values (186009099 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 77523 | 190 | 9779 | 482.15 | 374 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF301UTR.bed.gz | 1.49 MB | 8d8f9bec479ab88e1cd75e36ba648907 |
| ENCFF301UTR.tabix.bed.gz | 773.27 KB | 7533e6ec2eaf5b9b6f6a81e512993133 |
| ENCFF301UTR.tabix.bed.gz.tbi | 266.22 KB | 4f403a9fb426aa74452286b69ba679a0 |
| genomic_resource.yaml | 3.67 KB | ced329d60084f45074a9c7ad21c5b162 |
| statistics/ |