Resource
| Id | Histone_ChIP-seq/ENCSR301VIW |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR301VIW [biosample_summary="Homo sapiens smooth muscle cell originated from H9" and target="H2AFZ"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: female embryo (5 days) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN940WYC|/analyses/ENCAN940WYC/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_internal_action: Released analysis {ENCAN940WYC|/analyses/ENCAN940WYC/} has in progress subobject document {63814262-4f86-43e5-b2bc-e48e34fb9afe|/documents/63814262-4f86-43e5-b2bc-e48e34fb9afe/} audit_warning: Processed alignments file {ENCFF328EIH|/files/ENCFF328EIH/} processed by ChIP-seq ENCODE4 v1.6.0 GRCh38 pipeline has 19545308 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H2AFZ-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 {ENCFF093KSG|/files/ENCFF093KSG/} processed by ChIP-seq ENCODE4 v1.6.0 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 {ENCFF093KSG|/files/ENCFF093KSG/} processed by ChIP-seq ENCODE4 v1.6.0 GRCh38 pipeline was generated from a library with PBC2 value of 9.81. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR301VIW | float |
Histone_ChIP-seq_ENCSR301VIW |
Histone_ChIP-seq ENCSR301VIW [biosample_summary="Homo sapiens smooth muscle cell originated from H9" and target="H2AFZ"]
|
 |
[1.54, 15.1] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 55217173 | 1.72% | 74531 |
| chr1 | 4489661 | 1.80% | 6007 |
| chr2 | 4710811 | 1.95% | 6367 |
| chr3 | 3672533 | 1.85% | 4910 |
| chr4 | 4338223 | 2.28% | 5995 |
| chr5 | 3630169 | 2.00% | 4918 |
| chr6 | 4279613 | 2.51% | 5559 |
| chr7 | 3086899 | 1.94% | 4224 |
| chr8 | 2890480 | 1.99% | 3991 |
| chr9 | 2043143 | 1.48% | 2792 |
| chr10 | 2474103 | 1.85% | 3247 |
| chr11 | 2424426 | 1.79% | 3288 |
| chr12 | 3037676 | 2.28% | 4050 |
| chr13 | 1915989 | 1.68% | 2693 |
| chr14 | 1866838 | 1.74% | 2450 |
| chr15 | 1511675 | 1.48% | 1987 |
| chr16 | 1141773 | 1.26% | 1559 |
| chr17 | 1565560 | 1.88% | 2129 |
| chr18 | 1435401 | 1.79% | 1993 |
| chr19 | 1184510 | 2.02% | 1565 |
| chr20 | 1046030 | 1.62% | 1392 |
| chr21 | 635842 | 1.36% | 923 |
| chr22 | 513320 | 1.01% | 714 |
| chrX | 1322498 | 0.85% | 1778 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 74531 | 205 | 9033 | 740.86 | 617 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF233ZZY.bed.gz | 1.77 MB | a9b9832484b15ce9a6dc63bbb1f9fb28 |
| ENCFF233ZZY.tabix.bed.gz | 806.22 KB | 47738aecd57ac46246877feaba0d991c |
| ENCFF233ZZY.tabix.bed.gz.tbi | 333.14 KB | a7dc8d80fb2f876314d8d576925688b8 |
| genomic_resource.yaml | 3.47 KB | a1a7bd82524c28423b77a9233cd64a13 |
| statistics/ |