Resource
| Id | Histone_ChIP-seq/ENCSR000DWF |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000DWF [biosample_summary="Homo sapiens LNCaP clone FGC" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN146MKZ|/analyses/ENCAN146MKZ/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_internal_action: Released analysis {ENCAN146MKZ|/analyses/ENCAN146MKZ/} has in progress subobject document {ad9c34c3-c7c9-4fe5-bf74-395d10982562|/documents/ad9c34c3-c7c9-4fe5-bf74-395d10982562/} audit_warning: Processed alignments file {ENCFF934RQP|/files/ENCFF934RQP/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 13431325 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 {ENCFF303WWR|/files/ENCFF303WWR/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 15852615 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 {ENCFF934RQP|/files/ENCFF934RQP/} 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 {ENCFF934RQP|/files/ENCFF934RQP/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC2 value of 7.25. 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 {ENCFF303WWR|/files/ENCFF303WWR/} 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 {ENCFF303WWR|/files/ENCFF303WWR/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC2 value of 7.31. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000DWF | float |
Histone_ChIP-seq_ENCSR000DWF |
Histone_ChIP-seq ENCSR000DWF [biosample_summary="Homo sapiens LNCaP clone FGC" and target="H3K4me3"]
|
 |
[1.84, 174] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 36553763 | 1.14% | 26099 |
| chr1 | 3623382 | 1.46% | 2534 |
| chr2 | 2237232 | 0.92% | 1680 |
| chr3 | 1994112 | 1.01% | 1399 |
| chr4 | 1554804 | 0.82% | 1144 |
| chr5 | 1737514 | 0.96% | 1230 |
| chr6 | 2089157 | 1.22% | 1441 |
| chr7 | 1713122 | 1.08% | 1301 |
| chr8 | 1377689 | 0.95% | 1044 |
| chr9 | 1509377 | 1.09% | 1118 |
| chr10 | 1533350 | 1.15% | 1149 |
| chr11 | 1912206 | 1.42% | 1292 |
| chr12 | 1867709 | 1.40% | 1260 |
| chr13 | 693028 | 0.61% | 547 |
| chr14 | 1200097 | 1.12% | 868 |
| chr15 | 1202793 | 1.18% | 861 |
| chr16 | 1561306 | 1.73% | 1095 |
| chr17 | 2144195 | 2.58% | 1427 |
| chr18 | 623939 | 0.78% | 482 |
| chr19 | 2453907 | 4.19% | 1648 |
| chr20 | 970110 | 1.51% | 717 |
| chr21 | 489676 | 1.05% | 383 |
| chr22 | 887587 | 1.75% | 652 |
| chrX | 1116820 | 0.72% | 793 |
| chrY | 60651 | 0.11% | 34 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 26099 | 208 | 29233 | 1400.58 | 1030 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF586HAM.bed.gz | 694.45 KB | 28643b679bd78766df8d267f4ab81573 |
| ENCFF586HAM.tabix.bed.gz | 302.49 KB | 818e5f3b146a345ca2c2c3bb99e7bba8 |
| ENCFF586HAM.tabix.bed.gz.tbi | 156.91 KB | 295f3c36c8bb79853d2da4f0b3054840 |
| genomic_resource.yaml | 5.25 KB | 42eb6504e07a276df332ac8990ea17f1 |
| statistics/ |