Resource
| Id | Histone_ChIP-seq/ENCSR000DVG |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000DVG [biosample_summary="Homo sapiens kidney epithelial cell" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN644AAA|/analyses/ENCAN644AAA/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_internal_action: Released analysis {ENCAN644AAA|/analyses/ENCAN644AAA/} has in progress subobject document {21e57bec-6d47-4f03-aef6-0e2d81f72313|/documents/21e57bec-6d47-4f03-aef6-0e2d81f72313/} audit_warning: Processed alignments file {ENCFF222GZJ|/files/ENCFF222GZJ/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 10742571 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 {ENCFF925WTZ|/files/ENCFF925WTZ/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 12081735 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 {ENCFF222GZJ|/files/ENCFF222GZJ/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.86. 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 {ENCFF222GZJ|/files/ENCFF222GZJ/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC2 value of 7.55. 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 {ENCFF925WTZ|/files/ENCFF925WTZ/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.87. 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 {ENCFF925WTZ|/files/ENCFF925WTZ/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC2 value of 8.17. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000DVG | float |
Histone_ChIP-seq_ENCSR000DVG |
Histone_ChIP-seq ENCSR000DVG [biosample_summary="Homo sapiens kidney epithelial cell" and target="H3K4me3"]
|
 |
[1.95, 170] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 32189613 | 1.00% | 25751 |
| chr1 | 3141037 | 1.26% | 2559 |
| chr2 | 2282017 | 0.94% | 1755 |
| chr3 | 1853929 | 0.93% | 1411 |
| chr4 | 1336220 | 0.70% | 997 |
| chr5 | 1540897 | 0.85% | 1165 |
| chr6 | 1959978 | 1.15% | 1495 |
| chr7 | 1605863 | 1.01% | 1282 |
| chr8 | 1214870 | 0.84% | 943 |
| chr9 | 1319102 | 0.95% | 1111 |
| chr10 | 1393340 | 1.04% | 1089 |
| chr11 | 1691037 | 1.25% | 1351 |
| chr12 | 1678224 | 1.26% | 1266 |
| chr13 | 670318 | 0.59% | 519 |
| chr14 | 1042298 | 0.97% | 830 |
| chr15 | 1033103 | 1.01% | 846 |
| chr16 | 1229550 | 1.36% | 1007 |
| chr17 | 1863219 | 2.24% | 1473 |
| chr18 | 577330 | 0.72% | 443 |
| chr19 | 1953881 | 3.33% | 1788 |
| chr20 | 802087 | 1.24% | 646 |
| chr21 | 313870 | 0.67% | 260 |
| chr22 | 668992 | 1.32% | 596 |
| chrX | 1018451 | 0.65% | 919 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 25751 | 148 | 20350 | 1250.03 | 1026 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF855GTI.bed.gz | 697.75 KB | d715df6cdbbdc4733b858a3cf303a813 |
| ENCFF855GTI.tabix.bed.gz | 299.58 KB | e66dc41568811abc0518a62ed14a7002 |
| ENCFF855GTI.tabix.bed.gz.tbi | 147.63 KB | d7d9fc39c03e64bd0eaf55643bd686a9 |
| genomic_resource.yaml | 5.57 KB | 66470acde1600b6fe6f6e5d83a923ef7 |
| statistics/ |