Resource
| Id | Histone_ChIP-seq/ENCSR000DTE |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000DTE [biosample_summary="Homo sapiens cardiac fibroblast" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Released analysis {ENCAN593HII|/analyses/ENCAN593HII/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_internal_action: Released analysis {ENCAN593HII|/analyses/ENCAN593HII/} has in progress subobject document {c3309358-3462-45d9-8d16-5d8eb04d4dab|/documents/c3309358-3462-45d9-8d16-5d8eb04d4dab/} audit_warning: Processed alignments file {ENCFF383HTH|/files/ENCFF383HTH/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 13596821 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: Processed alignments file {ENCFF489CJB|/files/ENCFF489CJB/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 19632912 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 {ENCFF383HTH|/files/ENCFF383HTH/} processed by ChIP-seq ENCODE4 v1.5.1 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 {ENCFF383HTH|/files/ENCFF383HTH/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC2 value of 6.76. 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 {ENCFF489CJB|/files/ENCFF489CJB/} processed by ChIP-seq ENCODE4 v1.5.1 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 {ENCFF489CJB|/files/ENCFF489CJB/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC2 value of 5.64. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000DTE | float |
Histone_ChIP-seq_ENCSR000DTE |
Histone_ChIP-seq ENCSR000DTE [biosample_summary="Homo sapiens cardiac fibroblast" and target="H3K4me3"]
|
 |
[2.07, 163] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 30053952 | 0.93% | 28982 |
| chr1 | 2972841 | 1.19% | 2913 |
| chr2 | 2038260 | 0.84% | 1938 |
| chr3 | 1718447 | 0.87% | 1580 |
| chr4 | 1229808 | 0.65% | 1094 |
| chr5 | 1444952 | 0.80% | 1283 |
| chr6 | 1802685 | 1.06% | 1640 |
| chr7 | 1434214 | 0.90% | 1402 |
| chr8 | 1134894 | 0.78% | 1085 |
| chr9 | 1247790 | 0.90% | 1252 |
| chr10 | 1275527 | 0.95% | 1215 |
| chr11 | 1661992 | 1.23% | 1544 |
| chr12 | 1604509 | 1.20% | 1452 |
| chr13 | 584604 | 0.51% | 558 |
| chr14 | 959705 | 0.90% | 919 |
| chr15 | 980193 | 0.96% | 978 |
| chr16 | 1160029 | 1.28% | 1186 |
| chr17 | 1725567 | 2.07% | 1711 |
| chr18 | 499904 | 0.62% | 504 |
| chr19 | 1985978 | 3.39% | 2028 |
| chr20 | 756908 | 1.17% | 757 |
| chr21 | 270565 | 0.58% | 293 |
| chr22 | 641315 | 1.26% | 694 |
| chrX | 888691 | 0.57% | 927 |
| chrY | 34574 | 0.06% | 29 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 28982 | 153 | 10981 | 1036.99 | 766 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF532VDS.bed.gz | 673.84 KB | 3409b1952d68def666687f671283d892 |
| ENCFF532VDS.tabix.bed.gz | 312.87 KB | 08ff94c1c565c42ca4a0bb32ecd4676f |
| ENCFF532VDS.tabix.bed.gz.tbi | 148.14 KB | d1bf2268efb3fa5661722f7ce02ac80d |
| genomic_resource.yaml | 5.46 KB | 1d8e277fca8f544fa62f765039769c80 |
| statistics/ |