Resource
| Id | Histone_ChIP-seq/ENCSR858LJY |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR858LJY [biosample_summary="Homo sapiens muscle layer of colon tissue female adult (56 years)" and target="H3K27me3"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (56 years) output_type: pseudoreplicated peaks audit_internal_action: Archived analysis {ENCAN834SKG|/analyses/ENCAN834SKG/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed redacted alignments file {ENCFF693JZD|/files/ENCFF693JZD/} processed by ChIP-seq ENCODE3 hg19 pipeline has 26995134 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 redacted alignments file {ENCFF693JZD|/files/ENCFF693JZD/} processed by ChIP-seq ENCODE3 hg19 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 redacted alignments file {ENCFF693JZD|/files/ENCFF693JZD/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 6.61. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR858LJY | float |
Histone_ChIP-seq_ENCSR858LJY |
Histone_ChIP-seq ENCSR858LJY [biosample_summary="Homo sapiens muscle layer of colon tissue female adult (56 years)" and target="H3K27me3"]
|
 |
[1.75, 19] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 24757040 | 0.77% | 23458 |
| chr1 | 2513237 | 1.01% | 2421 |
| chr2 | 1367106 | 0.56% | 1142 |
| chr3 | 785257 | 0.40% | 683 |
| chr4 | 804780 | 0.42% | 670 |
| chr5 | 1157723 | 0.64% | 991 |
| chr6 | 1230230 | 0.72% | 1036 |
| chr7 | 1156629 | 0.73% | 988 |
| chr8 | 954297 | 0.66% | 864 |
| chr9 | 1045419 | 0.76% | 918 |
| chr10 | 1074631 | 0.80% | 914 |
| chr11 | 1184952 | 0.88% | 1077 |
| chr12 | 1104989 | 0.83% | 981 |
| chr13 | 472884 | 0.41% | 396 |
| chr14 | 706210 | 0.66% | 595 |
| chr15 | 646879 | 0.63% | 593 |
| chr16 | 1012958 | 1.12% | 939 |
| chr17 | 1612788 | 1.94% | 1484 |
| chr18 | 325612 | 0.41% | 324 |
| chr19 | 1768624 | 3.02% | 1600 |
| chr20 | 1107533 | 1.72% | 1120 |
| chr21 | 286228 | 0.61% | 285 |
| chr22 | 755814 | 1.49% | 867 |
| chrX | 1681515 | 1.08% | 2569 |
| chrY | 745 | <0.01% | 1 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 23458 | 310 | 31840 | 1055.38 | 680 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF582OJN.bed.gz | 466.08 KB | 7745882d274b1be236731b1b9d3eb453 |
| ENCFF582OJN.tabix.bed.gz | 238.41 KB | 5291bf0b45a05c90eb0e8eb11e70915a |
| ENCFF582OJN.tabix.bed.gz.tbi | 93.87 KB | c474683d720b4b27007968e1389124da |
| genomic_resource.yaml | 3.3 KB | c232be4b1cc55d8378da756178ab70a5 |
| statistics/ |