Resource
| Id | Histone_ChIP-seq/ENCSR561YSH |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR561YSH [biosample_summary="Homo sapiens sigmoid colon tissue male adult (34 years)" and target="H3K27ac"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (34 years) output_type: pseudoreplicated peaks audit_internal_action: Archived analysis {ENCAN603HQN|/analyses/ENCAN603HQN/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_warning: Processed alignments file {ENCFF012NGZ|/files/ENCFF012NGZ/} processed by ChIP-seq ENCODE3 hg19 pipeline has 18806875 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K27ac-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 {ENCFF012NGZ|/files/ENCFF012NGZ/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.84. 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 {ENCFF012NGZ|/files/ENCFF012NGZ/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 7.05. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR561YSH | float |
Histone_ChIP-seq_ENCSR561YSH |
Histone_ChIP-seq ENCSR561YSH [biosample_summary="Homo sapiens sigmoid colon tissue male adult (34 years)" and target="H3K27ac"]
|
 |
[1.42, 88.2] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 48474078 | 1.51% | 86322 |
| chr1 | 5018450 | 2.02% | 8748 |
| chr2 | 3428892 | 1.42% | 6399 |
| chr3 | 2441326 | 1.23% | 4672 |
| chr4 | 1466116 | 0.77% | 2800 |
| chr5 | 2177715 | 1.20% | 3979 |
| chr6 | 2408355 | 1.41% | 4571 |
| chr7 | 2105723 | 1.32% | 3804 |
| chr8 | 1699636 | 1.17% | 3313 |
| chr9 | 2301059 | 1.66% | 4024 |
| chr10 | 2243593 | 1.68% | 4138 |
| chr11 | 2864796 | 2.12% | 4801 |
| chr12 | 2305801 | 1.73% | 4002 |
| chr13 | 870933 | 0.76% | 1695 |
| chr14 | 1721904 | 1.61% | 3107 |
| chr15 | 1659847 | 1.63% | 3064 |
| chr16 | 2241718 | 2.48% | 3879 |
| chr17 | 3282940 | 3.94% | 5221 |
| chr18 | 765069 | 0.95% | 1511 |
| chr19 | 2861154 | 4.88% | 4374 |
| chr20 | 1500716 | 2.33% | 2731 |
| chr21 | 671102 | 1.44% | 1224 |
| chr22 | 1456214 | 2.87% | 2424 |
| chrX | 946013 | 0.61% | 1776 |
| chrY | 35006 | 0.06% | 65 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 86322 | 140 | 9126 | 561.55 | 371 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF962IBR.bed.gz | 1.97 MB | 83bfe316873b726f9b0ed1e6efa5877e |
| ENCFF962IBR.tabix.bed.gz | 903.2 KB | a4f1eab936283d2d2ae06b25d630bc46 |
| ENCFF962IBR.tabix.bed.gz.tbi | 236.91 KB | 3b80c99973da5b7ab3cdb46fb97a9cc3 |
| genomic_resource.yaml | 3.23 KB | fc12f9a4edc73d9bc0588f2e5851e68d |
| statistics/ |