Resource
| Id | Histone_ChIP-seq/ENCSR269OVV |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR269OVV [biosample_summary="Homo sapiens B cell" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_error: Processed alignments file {ENCFF194EUZ|/files/ENCFF194EUZ/} processed by ChIP-seq ENCODE3 hg19 pipeline has 2714503 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me3-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_internal_action: Archived analysis {ENCAN127DII|/analyses/ENCAN127DII/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF166EMH|/files/ENCFF166EMH/} processed by ChIP-seq ENCODE3 hg19 pipeline has 6801933 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me3-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 {ENCFF166EMH|/files/ENCFF166EMH/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.84. 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 {ENCFF166EMH|/files/ENCFF166EMH/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 6.01. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR269OVV | float |
Histone_ChIP-seq_ENCSR269OVV |
Histone_ChIP-seq ENCSR269OVV [biosample_summary="Homo sapiens B cell" and target="H3K4me3"]
|
 |
[2.11, 41.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 20760486 | 0.65% | 31060 |
| chr1 | 2171332 | 0.87% | 3114 |
| chr2 | 1530313 | 0.63% | 2195 |
| chr3 | 1231941 | 0.62% | 1800 |
| chr4 | 871458 | 0.46% | 1226 |
| chr5 | 1037371 | 0.57% | 1434 |
| chr6 | 1455834 | 0.85% | 1961 |
| chr7 | 969159 | 0.61% | 1454 |
| chr8 | 744786 | 0.51% | 1154 |
| chr9 | 762784 | 0.55% | 1248 |
| chr10 | 853574 | 0.64% | 1320 |
| chr11 | 1076163 | 0.80% | 1583 |
| chr12 | 1198478 | 0.90% | 1698 |
| chr13 | 465185 | 0.41% | 692 |
| chr14 | 692080 | 0.65% | 1001 |
| chr15 | 687768 | 0.67% | 1045 |
| chr16 | 733731 | 0.81% | 1222 |
| chr17 | 1106685 | 1.33% | 1739 |
| chr18 | 315652 | 0.39% | 508 |
| chr19 | 1258272 | 2.15% | 2005 |
| chr20 | 488205 | 0.76% | 782 |
| chr21 | 214247 | 0.46% | 363 |
| chr22 | 381525 | 0.75% | 653 |
| chrX | 491845 | 0.32% | 837 |
| chrY | 22098 | 0.04% | 26 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 31060 | 155 | 9764 | 668.4 | 479 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF348DYH.bed.gz | 606.28 KB | c00d1bf27d58933340e1ae186848640b |
| ENCFF348DYH.tabix.bed.gz | 317.26 KB | ee8b254fd63c505df8e6cf8e79909027 |
| ENCFF348DYH.tabix.bed.gz.tbi | 140.16 KB | e96423af8f270ec3addc88ebb9d9c8ef |
| genomic_resource.yaml | 3.66 KB | e9dd8e55a2019f9ac34e5afd12b7b8ab |
| statistics/ |