Resource
| Id | Histone_ChIP-seq/ENCSR042RIW |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR042RIW [biosample_summary="Homo sapiens sigmoid colon 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: Archived analysis {ENCAN709DNO|/analyses/ENCAN709DNO/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF454NHC|/files/ENCFF454NHC/} processed by ChIP-seq ENCODE3 hg19 pipeline has 15129849 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 {ENCFF454NHC|/files/ENCFF454NHC/} processed by ChIP-seq ENCODE3 hg19 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 {ENCFF454NHC|/files/ENCFF454NHC/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 8.39. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR042RIW | float |
Histone_ChIP-seq_ENCSR042RIW |
Histone_ChIP-seq ENCSR042RIW [biosample_summary="Homo sapiens sigmoid colon tissue male adult (34 years)" and target="H3K27me3"]
|
 |
[1.39, 17.3] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 8918799 | 0.28% | 24347 |
| chr1 | 800498 | 0.32% | 2210 |
| chr2 | 682107 | 0.28% | 1821 |
| chr3 | 375421 | 0.19% | 1100 |
| chr4 | 380618 | 0.20% | 1038 |
| chr5 | 488585 | 0.27% | 1371 |
| chr6 | 459561 | 0.27% | 1274 |
| chr7 | 474257 | 0.30% | 1297 |
| chr8 | 386605 | 0.27% | 1045 |
| chr9 | 420941 | 0.30% | 1125 |
| chr10 | 497550 | 0.37% | 1265 |
| chr11 | 463198 | 0.34% | 1266 |
| chr12 | 401619 | 0.30% | 1136 |
| chr13 | 219614 | 0.19% | 607 |
| chr14 | 260436 | 0.24% | 715 |
| chr15 | 265767 | 0.26% | 710 |
| chr16 | 308455 | 0.34% | 833 |
| chr17 | 522801 | 0.63% | 1345 |
| chr18 | 163766 | 0.20% | 489 |
| chr19 | 527595 | 0.90% | 1368 |
| chr20 | 366542 | 0.57% | 983 |
| chr21 | 120491 | 0.26% | 359 |
| chr22 | 235531 | 0.46% | 646 |
| chrX | 94727 | 0.06% | 336 |
| chrY | 2114 | <0.01% | 8 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 24347 | 130 | 4543 | 366.32 | 279 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF516BID.bed.gz | 478.2 KB | ee9e5cac8cb3f26430cff08497f19d24 |
| ENCFF516BID.tabix.bed.gz | 239.42 KB | adf6024ced84e3a4e486b10ac30624a1 |
| ENCFF516BID.tabix.bed.gz.tbi | 121.08 KB | cc992ea4f4ea22d9a62ee2f471b282c9 |
| genomic_resource.yaml | 3.24 KB | 2a0884f5088b79e6af8dcdb7f174a2a8 |
| statistics/ |