Resource
| Id | Histone_ChIP-seq/ENCSR000DWL |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000DWL [biosample_summary="Homo sapiens CD14-positive monocyte female" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 1 summary: female output_type: pseudoreplicated peaks audit_internal_action: Archived analysis {ENCAN884RLB|/analyses/ENCAN884RLB/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_warning: Processed alignments file {ENCFF764OBU|/files/ENCFF764OBU/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 16347826 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 {ENCFF764OBU|/files/ENCFF764OBU/} 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 {ENCFF764OBU|/files/ENCFF764OBU/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 6.19. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000DWL | float |
Histone_ChIP-seq_ENCSR000DWL |
Histone_ChIP-seq ENCSR000DWL [biosample_summary="Homo sapiens CD14-positive monocyte female" and target="H3K4me3"]
|
 |
[1.69, 110] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 27649276 | 0.86% | 27045 |
| chr1 | 2797303 | 1.12% | 2715 |
| chr1_KI270712v1_random | 971 | 0.55% | 2 |
| chr2 | 1913787 | 0.79% | 1847 |
| chr3 | 1640260 | 0.83% | 1602 |
| chr4 | 1126334 | 0.59% | 1052 |
| chr5 | 1307485 | 0.72% | 1192 |
| chr6 | 1761748 | 1.03% | 1657 |
| chr7 | 1321755 | 0.83% | 1331 |
| chr8 | 1019018 | 0.70% | 1022 |
| chr9 | 1122418 | 0.81% | 1123 |
| chr10 | 1156709 | 0.86% | 1079 |
| chr11 | 1471245 | 1.09% | 1396 |
| chr12 | 1560891 | 1.17% | 1448 |
| chr13 | 606757 | 0.53% | 590 |
| chr14 | 876060 | 0.82% | 833 |
| chr15 | 877841 | 0.86% | 866 |
| chr16 | 1022126 | 1.13% | 1050 |
| chr17 | 1548011 | 1.86% | 1537 |
| chr17_GL000205v2_random | 1432 | 0.77% | 2 |
| chr18 | 461580 | 0.57% | 494 |
| chr19 | 1627097 | 2.78% | 1705 |
| chr20 | 691734 | 1.07% | 708 |
| chr21 | 300998 | 0.64% | 308 |
| chr22 | 551190 | 1.08% | 580 |
| chrUn_GL000218v1 | 333 | 0.21% | 1 |
| chrUn_GL000219v1 | 1578 | 0.88% | 3 |
| chrX | 882615 | 0.57% | 902 |
| 3339 contigs with no values (185602521 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 27045 | 185 | 10980 | 1022.34 | 766 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF755NQZ.bed.gz | 739.83 KB | 08f7a20517d225527b476c5be188ad61 |
| ENCFF755NQZ.tabix.bed.gz | 312.06 KB | 285c93a64703c2ff7f36c519f9996267 |
| ENCFF755NQZ.tabix.bed.gz.tbi | 153.46 KB | 663fcbd9e4f6420b0cf4c89a1d9b0e47 |
| genomic_resource.yaml | 3.17 KB | a7ce83fdd79349f775133f08781ac314 |
| statistics/ |