Resource
| Id | Histone_ChIP-seq/ENCSR322MEI |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR322MEI [biosample_summary="Homo sapiens H1" and target="H3K4me2"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN642WLT|/analyses/ENCAN642WLT/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_internal_action: Released analysis {ENCAN642WLT|/analyses/ENCAN642WLT/} has in progress subobject document {6663902f-14f4-46c1-b44a-d7f14f8636fc|/documents/6663902f-14f4-46c1-b44a-d7f14f8636fc/} audit_not_compliant: Processed alignments file {ENCFF080SQV|/files/ENCFF080SQV/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 9804090 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me2-human and investigated as a narrow histone mark is 10 million usable fragments. The recommended value is > 20 million, but > 10 million is acceptable. (See {ENCODE ChIP-seq data standards|/data-standards/chip-seq/}) audit_warning: Processed alignments file {ENCFF480QXG|/files/ENCFF480QXG/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 12381198 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me2-human and investigated as a narrow histone mark is 10 million usable fragments. The recommended value is > 20 million, but > 10 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 {ENCFF080SQV|/files/ENCFF080SQV/} processed by ChIP-seq ENCODE4 v1.6.1 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 {ENCFF080SQV|/files/ENCFF080SQV/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 6.75. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR322MEI | float |
Histone_ChIP-seq_ENCSR322MEI |
Histone_ChIP-seq ENCSR322MEI [biosample_summary="Homo sapiens H1" and target="H3K4me2"]
|
 |
[1.39, 53.2] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 88804594 | 2.76% | 49637 |
| chr1 | 8657275 | 3.48% | 4697 |
| chr2 | 6318534 | 2.61% | 3657 |
| chr3 | 5126409 | 2.59% | 2966 |
| chr4 | 3754877 | 1.97% | 2202 |
| chr5 | 4544738 | 2.50% | 2595 |
| chr6 | 5385824 | 3.15% | 2984 |
| chr7 | 4473727 | 2.81% | 2615 |
| chr8 | 3548231 | 2.44% | 2111 |
| chr9 | 3635382 | 2.63% | 2055 |
| chr10 | 3915187 | 2.93% | 2218 |
| chr11 | 4691109 | 3.47% | 2579 |
| chr12 | 4605022 | 3.46% | 2532 |
| chr13 | 1980033 | 1.73% | 1168 |
| chr14 | 2801594 | 2.62% | 1523 |
| chr15 | 2926250 | 2.87% | 1641 |
| chr16 | 3264365 | 3.61% | 1813 |
| chr17 | 4636829 | 5.57% | 2399 |
| chr18 | 1757509 | 2.19% | 1073 |
| chr19 | 4666376 | 7.96% | 2303 |
| chr20 | 2424715 | 3.76% | 1363 |
| chr21 | 826914 | 1.77% | 485 |
| chr22 | 1824499 | 3.59% | 1028 |
| chrX | 2945347 | 1.89% | 1581 |
| chrY | 93848 | 0.16% | 49 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 49637 | 435 | 28744 | 1789.08 | 1384 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF583ABZ.bed.gz | 1.31 MB | 0f731b909e1d5d9e2b46f1287802a38a |
| ENCFF583ABZ.tabix.bed.gz | 574.37 KB | 8ae8178ce8e88495fb1b30c3e6221e73 |
| ENCFF583ABZ.tabix.bed.gz.tbi | 255.78 KB | 0392313c1334c2f3c19df63f9804498e |
| genomic_resource.yaml | 3.91 KB | 09284a3de7124c1097efcbd3904467a0 |
| statistics/ |