Resource
| Id | Histone_ChIP-seq/ENCSR088GXB |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR088GXB [biosample_summary="Homo sapiens esophagus tissue male adult (34 years)" and target="H3K27me3"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (34 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN568CGE|/analyses/ENCAN568CGE/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_internal_action: Released analysis {ENCAN568CGE|/analyses/ENCAN568CGE/} has in progress subobject document {7bbc33e3-6e60-4889-ad61-3e96f1b3fe2d|/documents/7bbc33e3-6e60-4889-ad61-3e96f1b3fe2d/} audit_not_compliant: Processed alignments file {ENCFF643MDE|/files/ENCFF643MDE/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 23273011 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K27me3-human and investigated as a broad histone mark is 20 million usable fragments. The recommended value is > 45 million, but > 35 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 {ENCFF643MDE|/files/ENCFF643MDE/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.81. 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 {ENCFF643MDE|/files/ENCFF643MDE/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 5.38. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR088GXB | float |
Histone_ChIP-seq_ENCSR088GXB |
Histone_ChIP-seq ENCSR088GXB [biosample_summary="Homo sapiens esophagus tissue male adult (34 years)" and target="H3K27me3"]
|
 |
[1.87, 10.1] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 5899491 | 0.18% | 13349 |
| chr1 | 512223 | 0.21% | 1168 |
| chr2 | 512730 | 0.21% | 1104 |
| chr3 | 242937 | 0.12% | 569 |
| chr4 | 287210 | 0.15% | 666 |
| chr5 | 321673 | 0.18% | 762 |
| chr6 | 363879 | 0.21% | 868 |
| chr7 | 382463 | 0.24% | 810 |
| chr8 | 256832 | 0.18% | 605 |
| chr9 | 273367 | 0.20% | 610 |
| chr10 | 349360 | 0.26% | 754 |
| chr11 | 264827 | 0.20% | 592 |
| chr12 | 263502 | 0.20% | 626 |
| chr13 | 182342 | 0.16% | 402 |
| chr14 | 189192 | 0.18% | 423 |
| chr15 | 173790 | 0.17% | 406 |
| chr16 | 170759 | 0.19% | 414 |
| chr17 | 315506 | 0.38% | 644 |
| chr18 | 128176 | 0.16% | 302 |
| chr19 | 300469 | 0.51% | 647 |
| chr20 | 218156 | 0.34% | 495 |
| chr21 | 42471 | 0.09% | 109 |
| chr22 | 107964 | 0.21% | 262 |
| chrX | 39663 | 0.03% | 111 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 13349 | 155 | 5088 | 441.94 | 336 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF834PLN.bed.gz | 265.48 KB | acffaca473829f4d2aba62bc54b9cd95 |
| ENCFF834PLN.tabix.bed.gz | 135.06 KB | 482eb5de5603625f4b3927d2aa0aa30b |
| ENCFF834PLN.tabix.bed.gz.tbi | 71.71 KB | c675cefe9b8dea0d30641b97758f66e5 |
| genomic_resource.yaml | 3.47 KB | 7af46b54b7c0d8127a438441d72cbbbc |
| statistics/ |