Resource
| Id | Histone_ChIP-seq/ENCSR916MHZ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR916MHZ [biosample_summary="Homo sapiens iPS DF 6.9" and target="H3K27me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN809BCJ|/analyses/ENCAN809BCJ/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_internal_action: Released analysis {ENCAN809BCJ|/analyses/ENCAN809BCJ/} has in progress subobject document {8267c0bf-ace0-4b26-bd08-24b558af94d3|/documents/8267c0bf-ace0-4b26-bd08-24b558af94d3/} audit_not_compliant: Processed alignments file {ENCFF969MNW|/files/ENCFF969MNW/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 28666268 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_not_compliant: Processed alignments file {ENCFF101RJJ|/files/ENCFF101RJJ/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 20750818 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 {ENCFF969MNW|/files/ENCFF969MNW/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.89. 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 {ENCFF969MNW|/files/ENCFF969MNW/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 9.21. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR916MHZ | float |
Histone_ChIP-seq_ENCSR916MHZ |
Histone_ChIP-seq ENCSR916MHZ [biosample_summary="Homo sapiens iPS DF 6.9" and target="H3K27me3"]
|
 |
[1.64, 24.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 14274431 | 0.44% | 23273 |
| chr1 | 1346563 | 0.54% | 2338 |
| chr2 | 1134983 | 0.47% | 1713 |
| chr3 | 565919 | 0.29% | 1078 |
| chr4 | 734436 | 0.39% | 1114 |
| chr5 | 868962 | 0.48% | 1352 |
| chr6 | 905495 | 0.53% | 1432 |
| chr7 | 797984 | 0.50% | 1220 |
| chr8 | 592321 | 0.41% | 1023 |
| chr9 | 620408 | 0.45% | 1048 |
| chr10 | 848530 | 0.63% | 1261 |
| chr11 | 788752 | 0.58% | 1368 |
| chr12 | 813722 | 0.61% | 1188 |
| chr13 | 329195 | 0.29% | 568 |
| chr14 | 423619 | 0.40% | 743 |
| chr15 | 491892 | 0.48% | 744 |
| chr16 | 417403 | 0.46% | 639 |
| chr17 | 821236 | 0.99% | 1142 |
| chr18 | 274803 | 0.34% | 539 |
| chr19 | 387926 | 0.66% | 682 |
| chr20 | 358113 | 0.56% | 609 |
| chr21 | 106394 | 0.23% | 183 |
| chr22 | 364339 | 0.72% | 725 |
| chrX | 270787 | 0.17% | 544 |
| chrY | 10649 | 0.02% | 20 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 23273 | 120 | 20946 | 613.35 | 325 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF292KOH.bed.gz | 530.53 KB | bde0fed780f2fc17cf96dd9b7e2373b3 |
| ENCFF292KOH.tabix.bed.gz | 243.3 KB | 0b760c4f45f291eeafe3792931fafd02 |
| ENCFF292KOH.tabix.bed.gz.tbi | 74.36 KB | a6bdcda563e810032259711938a74f50 |
| genomic_resource.yaml | 3.94 KB | a880538bfd0da09b51b31c64f5e80a38 |
| statistics/ |